1
|
Borrelli W, Mei KJ, Park SJ, Schwartz BJ. Partial Molar Solvation Volume of the Hydrated Electron Simulated Via DFT. J Phys Chem B 2024; 128:2425-2431. [PMID: 38422045 PMCID: PMC10945486 DOI: 10.1021/acs.jpcb.3c05091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/03/2024] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
Different simulation models of the hydrated electron produce different solvation structures, but it has been challenging to determine which simulated solvation structure, if any, is the most comparable to experiment. In a recent work, Neupane et al. [J. Phys. Chem. B 2023, 127, 5941-5947] showed using Kirkwood-Buff theory that the partial molar volume of the hydrated electron, which is known experimentally, can be readily computed from an integral over the simulated electron-water radial distribution function. This provides a sensitive way to directly compare the hydration structure of different simulation models of the hydrated electron with experiment. Here, we compute the partial molar volume of an ab-initio-simulated hydrated electron model based on density-functional theory (DFT) with a hybrid functional at different simulated system sizes. We find that the partial molar volume of the DFT-simulated hydrated electron is not converged with respect to the system size for simulations with up to 128 waters. We show that even at the largest simulation sizes, the partial molar volume of DFT-simulated hydrated electrons is underestimated by a factor of 2 with respect to experiment, and at the standard 64-water size commonly used in the literature, DFT-based simulations underestimate the experimental solvation volume by a factor of ∼3.5. An extrapolation to larger box sizes does predict the experimental partial molar volume correctly; however, larger system sizes than those explored here are currently intractable without the use of machine-learned potentials. These results bring into question what aspects of the predicted hydrated electron radial distribution function, as calculated by DFT-based simulations with the PBEh-D3 functional, deviate from the true solvation structure.
Collapse
Affiliation(s)
| | | | - Sanghyun J. Park
- Department of Chemistry and
Biochemistry, University of California,
Los Angeles, Los Angeles, California 90095-1569, United States
| | - Benjamin J. Schwartz
- Department of Chemistry and
Biochemistry, University of California,
Los Angeles, Los Angeles, California 90095-1569, United States
| |
Collapse
|
2
|
Song S, Vuckovic S, Kim Y, Yu H, Sim E, Burke K. Extending density functional theory with near chemical accuracy beyond pure water. Nat Commun 2023; 14:799. [PMID: 36781855 PMCID: PMC9925738 DOI: 10.1038/s41467-023-36094-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/13/2023] [Indexed: 02/15/2023] Open
Abstract
Density functional simulations of condensed phase water are typically inaccurate, due to the inaccuracies of approximate functionals. A recent breakthrough showed that the SCAN approximation can yield chemical accuracy for pure water in all its phases, but only when its density is corrected. This is a crucial step toward first-principles biosimulations. However, weak dispersion forces are ubiquitous and play a key role in noncovalent interactions among biomolecules, but are not included in the new approach. Moreover, naïve inclusion of dispersion in HF-SCAN ruins its high accuracy for pure water. Here we show that systematic application of the principles of density-corrected DFT yields a functional (HF-r2SCAN-DC4) which recovers and not only improves over HF-SCAN for pure water, but also captures vital noncovalent interactions in biomolecules, making it suitable for simulations of solutions.
Collapse
Affiliation(s)
- Suhwan Song
- grid.15444.300000 0004 0470 5454Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722 Korea ,grid.266093.80000 0001 0668 7243Department of Chemistry, University of California, Irvine, CA 92697 USA
| | - Stefan Vuckovic
- grid.472716.10000 0004 1758 7362Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy ,grid.12380.380000 0004 1754 9227Departments of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Youngsam Kim
- grid.15444.300000 0004 0470 5454Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722 Korea
| | - Hayoung Yu
- grid.15444.300000 0004 0470 5454Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722 Korea
| | - Eunji Sim
- Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722, Korea.
| | - Kieron Burke
- grid.266093.80000 0001 0668 7243Department of Chemistry, University of California, Irvine, CA 92697 USA ,grid.266093.80000 0001 0668 7243Departments of Physics & Astronomy, University of California, Irvine, CA 92697 USA
| |
Collapse
|
3
|
Dasgupta S, Shahi C, Bhetwal P, Perdew JP, Paesani F. How Good Is the Density-Corrected SCAN Functional for Neutral and Ionic Aqueous Systems, and What Is So Right about the Hartree-Fock Density? J Chem Theory Comput 2022; 18:4745-4761. [PMID: 35785808 DOI: 10.1021/acs.jctc.2c00313] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density functional theory (DFT) is the most widely used electronic structure method, due to its simplicity and cost effectiveness. The accuracy of a DFT calculation depends not only on the choice of the density functional approximation (DFA) adopted but also on the electron density produced by the DFA. SCAN is a modern functional that satisfies all known constraints for meta-GGA functionals. The density-driven errors, defined as energy errors arising from errors of the self-consistent DFA electron density, can hinder SCAN from achieving chemical accuracy in some systems, including water. Density-corrected DFT (DC-DFT) can alleviate this shortcoming by adopting a more accurate electron density which, in most applications, is the electron density obtained at the Hartree-Fock level of theory due to its relatively low computational cost. In this work, we present extensive calculations aimed at determining the accuracy of the DC-SCAN functional for various aqueous systems. DC-SCAN (SCAN@HF) shows remarkable consistency in reproducing reference data obtained at the coupled cluster level of theory, with minimal loss of accuracy. Density-driven errors in the description of ionic aqueous clusters are thoroughly investigated. By comparison with the orbital-optimized CCD density in the water dimer, we find that the self-consistent SCAN density transfers a spurious fraction of an electron across the hydrogen bond to the hydrogen atom (H*, covalently bound to the donor oxygen atom) from the acceptor (OA) and donor (OD) oxygen atoms, while HF makes a much smaller spurious transfer in the opposite direction, consistent with DC-SCAN (SCAN@HF) reduction of SCAN overbinding due to delocalization error. While LDA seems to be the conventional extreme of density delocalization error, and HF the conventional extreme of (usually much smaller) density localization error, these two densities do not quite yield the conventional range of density-driven error in energy differences. Finally, comparisons of the DC-SCAN results with those obtained with the Fermi-Löwdin orbital self-interaction correction (FLOSIC) method show that DC-SCAN represents a more accurate approach to reducing density-driven errors in SCAN calculations of ionic aqueous clusters. While the HF density is superior to that of SCAN for noncompact water clusters, the opposite is true for the compact water molecule with exactly 10 electrons.
Collapse
Affiliation(s)
- Saswata Dasgupta
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Chandra Shahi
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Pradeep Bhetwal
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - John P Perdew
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States.,Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States.,Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States.,San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
| |
Collapse
|
4
|
Jana S, Constantin LA, Smiga S, Samal P. Solid-state performance of a meta-GGA screened hybrid density functional constructed from Pauli kinetic enhancement factor dependent semilocal exchange hole. J Chem Phys 2022; 157:024102. [DOI: 10.1063/5.0096674] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The semilocal form of the exchange hole is highly useful in developing non-local range-separated hybrid density functionals for finite and extended systems. The way to construct the conventional exact exchange hole model is based on either the Taylor series expansion or the reverse engineering technique from the corresponding exchange energy functional. Although the latter technique is quite popular in context of generalized gradient approximation (GGA) functionals, the same for the meta-GGA functionals is not so much explored. Thus, in this study, we propose a reverse-engineered semilocal exchange hole of a meta-GGA functional, that depends only on the meta-GGA ingredient α (also known as the Pauli kinetic energy enhancement factor). The model is used subsequently to design the short-range-separated meta-GGA hybrid density functional. We show that the present method can be successfully applied for several challenging problems in the context of solids, especially for which the GGA based hybrid fails drastically. This assessment proves that the present functional is quite useful for materials sciences. Finally, we also use this method for several molecular test cases, where the results are also as comparative as its base semilocal functional.
Collapse
Affiliation(s)
- Subrata Jana
- Department of Chemistry and Biochemistry, The Ohio State University, United States of America
| | - Lucian A. Constantin
- Istituto di Nanoscienze, Consiglio Nazionale delle Ricerche CNR-NANO, 41125 Modena, Italy, Italy
| | - Szymon Smiga
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University Institute of Physics, Poland
| | - Prasanjit Samal
- School of Physical Sciences, National Institute of Science Education and Research, India
| |
Collapse
|
5
|
Ghosh A, Jana S, Niranjan MK, Behera SK, Constantin LA, Samal P. Improved electronic structure prediction of chalcopyrite semiconductors from a semilocal density functional based on Pauli kinetic energy enhancement factor. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 34:075501. [PMID: 34768248 DOI: 10.1088/1361-648x/ac394d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
The correct treatment ofdelectrons is of prime importance in order to predict the electronic properties of the prototype chalcopyrite semiconductors. The effect ofdstates is linked with the anion displacement parameteru, which in turn influences the bandgap of these systems. Semilocal exchange-correlation functionals which yield good structural properties of semiconductors and insulators often fail to predict reasonableubecause of the underestimation of the bandgaps arising from the strong interplay betweendelectrons. In the present study, we show that the meta-generalized gradient approximation (meta-GGA) obtained from the cuspless hydrogen density (MGGAC) (2019Phys. Rev.B 100 155140) performs in an improved manner in apprehending the key features of the electronic properties of chalcopyrites, and its bandgaps are comparative to that obtained using state-of-art hybrid methods. Moreover, the present assessment also shows the importance of the Pauli kinetic energy enhancement factor,α= (τ-τW)/τunifin describing thedelectrons in chalcopyrites. The present study strongly suggests that the MGGAC functional within semilocal approximations can be a better and preferred choice to study the chalcopyrites and other solid-state systems due to its superior performance and significantly low computational cost.
Collapse
Affiliation(s)
- Arghya Ghosh
- Department of Physics, Indian Institute of Technology, Hyderabad, India
| | - Subrata Jana
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, United States of America
| | - Manish K Niranjan
- Department of Physics, Indian Institute of Technology, Hyderabad, India
| | - Sushant Kumar Behera
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| | - Lucian A Constantin
- Istituto di Nanoscienze, Consiglio Nazionale delle Ricerche CNR-NANO, 41125 Modena, Italy
| | - Prasanjit Samal
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| |
Collapse
|
6
|
Dasgupta S, Lambros E, Perdew JP, Paesani F. Elevating density functional theory to chemical accuracy for water simulations through a density-corrected many-body formalism. Nat Commun 2021; 12:6359. [PMID: 34737311 PMCID: PMC8569147 DOI: 10.1038/s41467-021-26618-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/08/2021] [Indexed: 11/09/2022] Open
Abstract
Density functional theory (DFT) has been extensively used to model the properties of water. Albeit maintaining a good balance between accuracy and efficiency, no density functional has so far achieved the degree of accuracy necessary to correctly predict the properties of water across the entire phase diagram. Here, we present density-corrected SCAN (DC-SCAN) calculations for water which, minimizing density-driven errors, elevate the accuracy of the SCAN functional to that of "gold standard" coupled-cluster theory. Building upon the accuracy of DC-SCAN within a many-body formalism, we introduce a data-driven many-body potential energy function, MB-SCAN(DC), that quantitatively reproduces coupled cluster reference values for interaction, binding, and individual many-body energies of water clusters. Importantly, molecular dynamics simulations carried out with MB-SCAN(DC) also reproduce the properties of liquid water, which thus demonstrates that MB-SCAN(DC) is effectively the first DFT-based model that correctly describes water from the gas to the liquid phase.
Collapse
Affiliation(s)
- Saswata Dasgupta
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Eleftherios Lambros
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - John P Perdew
- Department of Physics, Temple University, Philadelphia, PA, 19122, USA
- Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
- Materials Science and Engineering, University of California, San Diego, La Jolla, CA, 92093, USA.
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
7
|
Saito T, Yokoi T, Nakamura A, Matsunaga K. First-principles based theoretical calculations of atomic structures of hydroxyapatite surfaces and their charge states in contact with aqueous solutions. RSC Adv 2021; 11:34004-34014. [PMID: 35497313 PMCID: PMC9042352 DOI: 10.1039/d1ra06311a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/01/2021] [Indexed: 01/09/2023] Open
Abstract
Surface charge states of biomaterials are often important for the adsorption of cells, proteins, and foreign ions on their surfaces, which should be clarified at the atomic and electronic levels. First-principles calculations were performed to reveal thermodynamically stable surface atomic structures and their charge states in hydroxyapatite (HAp). Effects of aqueous environments on the surface stability were considered using an implicit solvation model. It was found that in an air atmosphere, stoichiometric {0001} and P-rich {101̄0} surfaces are energetically favorable, whereas in an aqueous solution, a Ca-rich {101̄0} surface is the most stable. This difference suggests that preferential surface structures strongly depend on chemical environments with and without aqueous solutions. Their surface potentials at zero charge were calculated to obtain the isoelectric points (pHPZC). pHPZC values for the {0001} surface and the Ca-rich {101̄0} surface were obtained to be 4.8 and 8.7, respectively. This indicates that in an aqueous solution at neutral pH, the {0001} and Ca-rich {101̄0} surfaces are negatively and positively charged, respectively. This trend agrees with experimental data from chromatography and zeta potential measurements. Our methodology based on first-principles calculations enables determining macroscopic charge states of HAp surfaces from atomic and electronic levels.
Collapse
Affiliation(s)
- T Saito
- Department of Materials Physics, Nagoya University Nagoya 464-8603 Japan
| | - T Yokoi
- Department of Materials Physics, Nagoya University Nagoya 464-8603 Japan
| | - A Nakamura
- Department of Materials Physics, Nagoya University Nagoya 464-8603 Japan
| | - K Matsunaga
- Department of Materials Physics, Nagoya University Nagoya 464-8603 Japan .,Nanostructures Research Laboratory, Japan Fine Ceramics Center Nagoya 456-8587 Japan
| |
Collapse
|
8
|
Jana S, Myneni H, Śmiga S, Constantin LA, Samal P. Benchmark test of a dispersion corrected revised Tao-Mo semilocal functional for thermochemistry, kinetics, and noncovalent interactions of molecules and solids. J Chem Phys 2021; 155:114102. [PMID: 34551544 DOI: 10.1063/5.0060538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In the density functional theory, dispersion corrected semilocal approximations are often used to benchmark weekly interacting finite and extended systems. Here, the focus is on providing a broad overview of the performance of D3 dispersion corrected revised Tao-Mo (revTM) semilocal functionals [A. Patra et al., J. Chem. Phys. 153, 084 117 (2020)] for thermochemistry and kinetics of molecules, molecular crystals, ice polymorphs, metal-organic systems, atom/molecular adsorption on solids, water interacting with nano-materials, binding energies of layered materials, and properties of weekly and strongly bonded solids. We show that the most suitable "optimized power" function for the revTM functional needs a modification to make it suitable for properties related to the diverse nature of finite and extended systems. The present work is an extension of the previously proposed revTM+D3 method with the motivation to design and benchmark the dispersion corrected cost-effective method based on this semilocal approximation. We show that the revised revTM+D3 functional provides various general purpose molecular and solid properties with the closest to experimental findings than its predecessor. The present assessment and benchmarking can be practically useful for performing cost-effective method based simulations of various molecular and solid-state properties.
Collapse
Affiliation(s)
- Subrata Jana
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752 050, India
| | - Hemanadhan Myneni
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Szymon Śmiga
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Toruń, Poland
| | - Lucian A Constantin
- Istituto di Nanoscienze, Consiglio Nazionale delle Ricerche CNR-NANO, 41125 Modena, Italy
| | - Prasanjit Samal
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752 050, India
| |
Collapse
|
9
|
Swann MT, Nicholas KM. Structural Effects on Dioxygen Evolution from Ru(V)−Oxo Complexes. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202100361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Matthew T. Swann
- Department of Chemistry and Biochemistry University of Oklahoma 101 Stephenson Parkway Norman OK 73069 USA
| | - Kenneth M. Nicholas
- Department of Chemistry and Biochemistry University of Oklahoma 101 Stephenson Parkway Norman OK 73069 USA
| |
Collapse
|
10
|
Jana S, Behera SK, Śmiga S, Constantin LA, Samal P. Accurate density functional made more versatile. J Chem Phys 2021; 155:024103. [PMID: 34266258 DOI: 10.1063/5.0051331] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We propose a one-electron self-interaction-free correlation energy functional compatible with the order-of-limit problem-free Tao-Mo (TM) semilocal functional (regTM) [J. Tao and Y. Mo, Phys. Rev. Lett. 117, 073001 (2016) and Patra et al., J. Chem. Phys. 153, 184112 (2020)] to be used for general purpose condensed matter physics and quantum chemistry. The assessment of the proposed functional for large classes of condensed matter and chemical systems shows its improvement in most cases compared to the TM functional, e.g., when applied to the relative energy difference of MnO2 polymorphs. In this respect, the present exchange-correction functional, which incorporates the TM technique of the exchange hole model combined with the slowly varying density correction, can achieve broad applicability, being able to solve difficult solid-state problems.
Collapse
Affiliation(s)
- Subrata Jana
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| | - Sushant Kumar Behera
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| | - Szymon Śmiga
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Toruń, Poland
| | - Lucian A Constantin
- Istituto di Nanoscienze, Consiglio Nazionale delle Ricerche CNR-NANO, 41125 Modena, Italy
| | - Prasanjit Samal
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| |
Collapse
|