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Duignan TT. The Potential of Neural Network Potentials. ACS PHYSICAL CHEMISTRY AU 2024; 4:232-241. [PMID: 38800721 PMCID: PMC11117678 DOI: 10.1021/acsphyschemau.4c00004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 05/29/2024]
Abstract
In the next half-century, physical chemistry will likely undergo a profound transformation, driven predominantly by the combination of recent advances in quantum chemistry and machine learning (ML). Specifically, equivariant neural network potentials (NNPs) are a breakthrough new tool that are already enabling us to simulate systems at the molecular scale with unprecedented accuracy and speed, relying on nothing but fundamental physical laws. The continued development of this approach will realize Paul Dirac's 80-year-old vision of using quantum mechanics to unify physics with chemistry and providing invaluable tools for understanding materials science, biology, earth sciences, and beyond. The era of highly accurate and efficient first-principles molecular simulations will provide a wealth of training data that can be used to build automated computational methodologies, using tools such as diffusion models, for the design and optimization of systems at the molecular scale. Large language models (LLMs) will also evolve into increasingly indispensable tools for literature review, coding, idea generation, and scientific writing.
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Baker S, Pagotto J, Duignan TT, Page AJ. High-Throughput Aqueous Electrolyte Structure Prediction Using IonSolvR and Equivariant Graph Neural Network Potentials. J Phys Chem Lett 2023; 14:9508-9515. [PMID: 37845640 DOI: 10.1021/acs.jpclett.3c01783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Neural network potentials have recently emerged as an efficient and accurate tool for accelerating ab initio molecular dynamics (AIMD) in order to simulate complex condensed phases such as electrolyte solutions. Their principal limitation, however, is their requirement for sufficiently large and accurate training sets, which are often composed of Kohn-Sham density functional theory (DFT) calculations. Here we examine the feasibility of using existing density functional tight-binding (DFTB) molecular dynamics trajectory data available in the IonSolvR database in order to accelerate the training of E(3)-equivariant graph neural network potentials. We show that the solvation structure of Na+ and Cl- in aqueous NaCl solutions can be accurately reproduced with remarkably small amounts of data (i.e., 100 MD frames). We further show that these predictions can be systematically improved further via an embarrassingly parallel resampling approach.
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Affiliation(s)
- Sophie Baker
- Discipline of Chemistry, College of Engineering, Science and Environment, University of Newcastle, Callaghan, Newcastle, NSW 2308, Australia
| | - Joshua Pagotto
- School of Chemical Engineering, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Timothy T Duignan
- School of Chemical Engineering, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Brisbane, QLD 4111, Australia
| | - Alister J Page
- Discipline of Chemistry, College of Engineering, Science and Environment, University of Newcastle, Callaghan, Newcastle, NSW 2308, Australia
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Hu F, He F, Yaron DJ. Treating Semiempirical Hamiltonians as Flexible Machine Learning Models Yields Accurate and Interpretable Results. J Chem Theory Comput 2023; 19:6185-6196. [PMID: 37705220 PMCID: PMC10536991 DOI: 10.1021/acs.jctc.3c00491] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Indexed: 09/15/2023]
Abstract
Quantum chemistry provides chemists with invaluable information, but the high computational cost limits the size and type of systems that can be studied. Machine learning (ML) has emerged as a means to dramatically lower the cost while maintaining high accuracy. However, ML models often sacrifice interpretability by using components such as the artificial neural networks of deep learning that function as black boxes. These components impart the flexibility needed to learn from large volumes of data but make it difficult to gain insight into the physical or chemical basis for the predictions. Here, we demonstrate that semiempirical quantum chemical (SEQC) models can learn from large volumes of data without sacrificing interpretability. The SEQC model is that of density-functional-based tight binding (DFTB) with fixed atomic orbital energies and interactions that are one-dimensional functions of the interatomic distance. This model is trained to ab initio data in a manner that is analogous to that used to train deep learning models. Using benchmarks that reflect the accuracy of the training data, we show that the resulting model maintains a physically reasonable functional form while achieving an accuracy, relative to coupled cluster energies with a complete basis set extrapolation (CCSD(T)*/CBS), that is comparable to that of density functional theory (DFT). This suggests that trained SEQC models can achieve a low computational cost and high accuracy without sacrificing interpretability. Use of a physically motivated model form also substantially reduces the amount of ab initio data needed to train the model compared to that required for deep learning models.
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Affiliation(s)
- Frank Hu
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Francis He
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - David J. Yaron
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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Kumar A, Craig VSJ, Robertson H, Page AJ, Webber GB, Wanless EJ, Mitchell VD, Andersson GG. Specific Ion Effects at the Vapor-Formamide Interface: A Reverse Hofmeister Series in Ion Concentration Depth Profiles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:12618-12626. [PMID: 37642667 DOI: 10.1021/acs.langmuir.3c01286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Employing neutral impact collision ion scattering spectroscopy (NICISS), we have directly measured the concentration depth profiles (CDPs) of various monovalent ions at the vapor-formamide interface. NICISS provides CDPs of individual ions by measuring the energy loss of neutral helium atoms backscattered from the solution interface. CDPs at the vapor-formamide interface of Cl-, Br-, I-, Na+, K+, and Cs+ are measured and compared to elucidate the interfacial specific ion trends. We report a reverse Hofmeister series in the presence of inorganic ions (anion and cation) at the vapor-formamide interface relative to the water-vapor interface, and the CDPs are found to be independent of the counterion for most ions studied. Thus, ions at the surface of formamide follow a "Hofmeister paradigm" where the counterion does not impact the ion series. These specific ion trends are complemented with surface tension and X-ray absorption near-edge structure (XANES) measurements on formamide electrolyte solutions.
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Affiliation(s)
- Anand Kumar
- Flinders Institute of Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia
| | - Vincent S J Craig
- Department of Materials Physics, Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia
| | - Hayden Robertson
- College of Science, Engineering, and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Alister J Page
- College of Science, Engineering, and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Grant B Webber
- College of Science, Engineering, and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Erica J Wanless
- College of Science, Engineering, and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | | | - Gunther G Andersson
- Flinders Institute of Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia
- Flinders Microscopy and Microanalysis, College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia
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Hercigonja M, Milovanović B, Etinski M, Petković M. Decorated crown ethers as selective ion traps: Solvent’s role in crown’s preference towards a specific ion. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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