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Goldman N, Fried LE, Lindsey RK, Pham CH, Dettori R. Enhancing the accuracy of density functional tight binding models through ChIMES many-body interaction potentials. J Chem Phys 2023; 158:144112. [PMID: 37061479 DOI: 10.1063/5.0141616] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
Semi-empirical quantum models such as Density Functional Tight Binding (DFTB) are attractive methods for obtaining quantum simulation data at longer time and length scales than possible with standard approaches. However, application of these models can require lengthy effort due to the lack of a systematic approach for their development. In this work, we discuss the use of the Chebyshev Interaction Model for Efficient Simulation (ChIMES) to create rapidly parameterized DFTB models, which exhibit strong transferability due to the inclusion of many-body interactions that might otherwise be inaccurate. We apply our modeling approach to silicon polymorphs and review previous work on titanium hydride. We also review the creation of a general purpose DFTB/ChIMES model for organic molecules and compounds that approaches hybrid functional and coupled cluster accuracy with two orders of magnitude fewer parameters than similar neural network approaches. In all cases, DFTB/ChIMES yields similar accuracy to the underlying quantum method with orders of magnitude improvement in computational cost. Our developments provide a way to create computationally efficient and highly accurate simulations over varying extreme thermodynamic conditions, where physical and chemical properties can be difficult to interrogate directly, and there is historically a significant reliance on theoretical approaches for interpretation and validation of experimental results.
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Affiliation(s)
- Nir Goldman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Laurence E Fried
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Rebecca K Lindsey
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - C Huy Pham
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - R Dettori
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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Goldman N, Kweon KE, Sadigh B, Heo TW, Lindsey RK, Pham CH, Fried LE, Aradi B, Holliday K, Jeffries JR, Wood BC. Semi-Automated Creation of Density Functional Tight Binding Models through Leveraging Chebyshev Polynomial-Based Force Fields. J Chem Theory Comput 2021; 17:4435-4448. [PMID: 34128678 DOI: 10.1021/acs.jctc.1c00172] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density functional tight binding (DFTB) is an attractive method for accelerated quantum simulations of condensed matter due to its enhanced computational efficiency over standard density functional theory (DFT) approaches. However, DFTB models can be challenging to determine for individual systems of interest, especially for metallic and interfacial systems where different bonding arrangements can lead to significant changes in electronic states. In this regard, we have created a rapid-screening approach for determining systematically improvable DFTB interaction potentials that can yield transferable models for a variety of conditions. Our method leverages a recent reactive molecular dynamics force field where many-body interactions are represented by linear combinations of Chebyshev polynomials. This allows for the efficient creation of multi-center representations with relative ease, requiring only a small investment in initial DFT calculations. We have focused our workflow on TiH2 as a model system and show that a relatively small training set based on unit-cell-sized calculations yields a model accurate for both bulk and surface properties. Our approach is easy to implement and can yield reliable DFTB models over a broad range of thermodynamic conditions, where physical and chemical properties can be difficult to interrogate directly and there is historically a significant reliance on theoretical approaches for interpretation and validation of experimental results.
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Affiliation(s)
- Nir Goldman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States.,Department of Chemical Engineering, University of California, Davis, Davis, California 95616, United States
| | - Kyoung E Kweon
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Babak Sadigh
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Tae Wook Heo
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Rebecca K Lindsey
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - C Huy Pham
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Laurence E Fried
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Bálint Aradi
- Bremen Center for Computational Materials Science, Universität Bremen, P.O.B. 330440, Bremen D-28334, Germany
| | - Kiel Holliday
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Jason R Jeffries
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Brandon C Wood
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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Kroonblawd MP, Lindsey RK, Goldman N. Synthesis of functionalized nitrogen-containing polycyclic aromatic hydrocarbons and other prebiotic compounds in impacting glycine solutions. Chem Sci 2019; 10:6091-6098. [PMID: 31360414 PMCID: PMC6585877 DOI: 10.1039/c9sc00155g] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/19/2019] [Indexed: 01/09/2023] Open
Abstract
Proteinogenic amino acids can be produced on or delivered to a planet via impacting abiotic sources and consequently were likely present before the emergence of life on Earth. However, the role that these materials played in prebiotic scenarios remains an open question, in part because little is known about the survivability and reactivity of astrophysical organic compounds upon impact with a planetary surface. To this end, we use a force-matched semi-empirical quantum simulation method to study impacts of aqueous proteinogenic amino acids at conditions reaching 48 GPa and 3000 K. Here, we probe a relatively unstudied mechanism for prebiotic synthesis where sudden heating and pressurization causes condensation of complex carbon-rich structures from mixtures of glycine, the simplest protein-forming amino acid. These carbon-containing clusters are stable on short timescales and undergo a fundamental structural transition upon expansion and cooling from predominantly sp3-bonded tetrahedral-like moieties to those that are more sp2-bonded and planar. The recovered sp2-bonded structures include large nitrogen containing polycyclic aromatic hydrocarbons (NPAHs) with a number of different functional groups and embedded bonded regions akin to oligo-peptides. A number of small organic molecules with prebiotic relevance are also predicted to form. This work presents an alternate route to gas-phase synthesis for the formation of NPAHs of high complexity and highlights the significance of both the thermodynamic path and local chemical self-assembly in forming prebiotic species during shock synthesis. Our results help determine the role of comets and other celestial bodies in both the delivery and synthesis of potentially significant life building compounds on early Earth.
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Affiliation(s)
- Matthew P Kroonblawd
- Physical and Life Sciences Directorate , Lawrence Livermore National Laboratory , Livermore , CA 94550 , USA .
| | - Rebecca K Lindsey
- Physical and Life Sciences Directorate , Lawrence Livermore National Laboratory , Livermore , CA 94550 , USA .
| | - Nir Goldman
- Physical and Life Sciences Directorate , Lawrence Livermore National Laboratory , Livermore , CA 94550 , USA .
- Department of Chemical Engineering , University of California , Davis , California 95616 , USA
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Force Matching Approaches to Extend Density Functional Theory to Large Time and Length Scales. COMPUTATIONAL APPROACHES FOR CHEMISTRY UNDER EXTREME CONDITIONS 2019. [DOI: 10.1007/978-3-030-05600-1_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Goldman N, Aradi B, Lindsey RK, Fried LE. Development of a Multicenter Density Functional Tight Binding Model for Plutonium Surface Hydriding. J Chem Theory Comput 2018; 14:2652-2660. [DOI: 10.1021/acs.jctc.8b00165] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nir Goldman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
| | - Bálint Aradi
- Bremen Center for Computational Materials Science, Universität Bremen, P.O.B. 330440, D-28334 Bremen, Germany
| | - Rebecca K. Lindsey
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Laurence E. Fried
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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Koziol L, Fried LE, Goldman N. Using Force Matching To Determine Reactive Force Fields for Water under Extreme Thermodynamic Conditions. J Chem Theory Comput 2016; 13:135-146. [DOI: 10.1021/acs.jctc.6b00707] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lucas Koziol
- Physical and Life Sciences
Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Laurence E. Fried
- Physical and Life Sciences
Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Nir Goldman
- Physical and Life Sciences
Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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Goldman N, Fried LE, Koziol L. Using Force-Matched Potentials To Improve the Accuracy of Density Functional Tight Binding for Reactive Conditions. J Chem Theory Comput 2015; 11:4530-5. [DOI: 10.1021/acs.jctc.5b00742] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nir Goldman
- Physical
and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Laurence E. Fried
- Physical
and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Lucas Koziol
- Physical
and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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Koziol L, Goldman N. PREBIOTIC HYDROCARBON SYNTHESIS IN IMPACTING REDUCED ASTROPHYSICAL ICY MIXTURES. ACTA ACUST UNITED AC 2015. [DOI: 10.1088/0004-637x/803/2/91] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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