1
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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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2
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Pham CH, Lindsey RK, Fried LE, Goldman N. High-Accuracy Semiempirical Quantum Models Based on a Minimal Training Set. J Phys Chem Lett 2022; 13:2934-2942. [PMID: 35343698 DOI: 10.1021/acs.jpclett.2c00453] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A great need exists for computationally efficient quantum simulation approaches that can achieve an accuracy similar to high-level theories at a fraction of the computational cost. In this regard, we have leveraged a machine-learned interaction potential based on Chebyshev polynomials to improve density functional tight binding (DFTB) models for organic materials. The benefit of our approach is two-fold: (1) many-body interactions can be corrected for in a systematic and rapidly tunable process, and (2) high-level quantum accuracy for a broad range of compounds can be achieved with ∼0.3% of data required for one advanced deep learning potential. Our model exhibits both transferability and extensibility through comparison to quantum chemical results for organic clusters, solid carbon phases, and molecular crystal phase stability rankings. Our efforts thus allow for high-throughput physical and chemical predictions with up to coupled-cluster accuracy for systems that are computationally intractable with standard approaches.
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Affiliation(s)
- Cong Huy Pham
- 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
| | - 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
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
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3
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Lindsey RK, Huy Pham C, Goldman N, Bastea S, Fried LE. Machine‐Learning a Solution for Reactive Atomistic Simulations of Energetic Materials. PROPELLANTS EXPLOSIVES PYROTECHNICS 2022. [DOI: 10.1002/prep.202200001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Rebecca K. Lindsey
- Physical and Life Sciences Directorate Lawrence Livermore National Laboratory Livermore California 94550 USA
| | - Cong Huy Pham
- Physical and Life Sciences Directorate Lawrence Livermore National Laboratory Livermore California 94550 USA
| | - Nir Goldman
- Physical and Life Sciences Directorate Lawrence Livermore National Laboratory Livermore California 94550 USA
- Department of Chemical Engineering University of California, Davis Davis California 95616 USA
| | - Sorin Bastea
- 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
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4
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Dettmann MA, Cavalcante LSR, Magdaleno C, Masalkovaitė K, Vong D, Dull JT, Rand BP, Daemen LL, Goldman N, Faller R, Moulé AJ. Comparing the Expense and Accuracy of Methods to Simulate Atomic Vibrations in Rubrene. J Chem Theory Comput 2021; 17:7313-7320. [PMID: 34818006 DOI: 10.1021/acs.jctc.1c00747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Atomic vibrations can inform about materials properties from hole transport in organic semiconductors to correlated disorder in metal-organic frameworks. Currently, there are several methods for predicting these vibrations using simulations, but the accuracy-efficiency tradeoffs have not been examined in depth. In this study, rubrene is used as a model system to predict atomic vibrational properties using six different simulation methods: density functional theory, density functional tight binding, density functional tight binding with a Chebyshev polynomial-based correction, a trained machine learning model, a pretrained machine learning model called ANI-1, and a classical forcefield model. The accuracy of each method is evaluated by comparison to the experimental inelastic neutron scattering spectrum. All methods discussed here show some accuracy across a wide energy region, though the Chebyshev-corrected tight-binding method showed the optimal combination of high accuracy with low expense. We then offer broad simulation guidelines to yield efficient, accurate results for inelastic neutron scattering spectrum prediction.
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Affiliation(s)
- Makena A Dettmann
- University of California Davis, Davis, California 95616, United States
| | | | - Corina Magdaleno
- University of California Davis, Davis, California 95616, United States
| | | | - Daniel Vong
- University of California Davis, Davis, California 95616, United States
| | - Jordan T Dull
- Department of Electrical Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Barry P Rand
- Department of Electrical Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Luke L Daemen
- Oak Ridge National Lab, Oak Ridge, Tennessee 37831, United States
| | - Nir Goldman
- University of California Davis, Davis, California 95616, United States.,Lawrence Livermore National Lab, Livermore, California 94550, United States
| | - Roland Faller
- University of California Davis, Davis, California 95616, United States
| | - Adam J Moulé
- University of California Davis, Davis, California 95616, United States
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5
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Kim B, Snyder R, Nagaraju M, Zhou Y, Ojeda-May P, Keeton S, Hege M, Shao Y, Pu J. Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force. J Chem Theory Comput 2021; 17:4961-4980. [PMID: 34283604 PMCID: PMC9064116 DOI: 10.1021/acs.jctc.1c00245] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
First-principles determination of free energy profiles for condensed-phase chemical reactions is hampered by the daunting costs associated with configurational sampling on ab initio quantum mechanical/molecular mechanical (AI/MM) potential energy surfaces. Here, we report a new method that enables efficient AI/MM free energy simulations through mean force fitting. In this method, a free energy path in collective variables (CVs) is first determined on an efficient reactive aiding potential. Based on the configurations sampled along the free energy path, correcting forces to reproduce the AI/MM forces on the CVs are determined through force matching. The AI/MM free energy profile is then predicted from simulations on the aiding potential in conjunction with the correcting forces. Such cycles of correction-prediction are repeated until convergence is established. As the instantaneous forces on the CVs sampled in equilibrium ensembles along the free energy path are fitted, this procedure faithfully restores the target free energy profile by reproducing the free energy mean forces. Due to its close connection with the reaction path-force matching (RP-FM) framework recently introduced by us, we designate the new method as RP-FM in collective variables (RP-FM-CV). We demonstrate the effectiveness of this method on a type-II solution-phase SN2 reaction, NH3 + CH3Cl (the Menshutkin reaction), simulated with an explicit water solvent. To obtain the AI/MM free energy profiles, we employed the semiempirical AM1/MM Hamiltonian as the base level for determining the string minimum free energy pathway, along which the free energy mean forces are fitted to various target AI/MM levels using the Hartree-Fock (HF) theory, density functional theory (DFT), and the second-order Møller-Plesset perturbation (MP2) theory as the AI method. The forces on the bond-breaking and bond-forming CVs at both the base and target levels are obtained by force transformation from Cartesian to redundant internal coordinates under the Wilson B-matrix formalism, where the linearized FM is facilitated by the use of spline functions. For the Menshutkin reaction tested, our FM treatment greatly reduces the deviations on the CV forces, originally in the range of 12-33 to ∼2 kcal/mol/Å. Comparisons with the experimental and benchmark AI/MM results, tests of the new method under a variety of simulation protocols, and analyses of the solute-solvent radial distribution functions suggest that RP-FM-CV can be used as an efficient, accurate, and robust method for simulating solution-phase chemical reactions.
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Affiliation(s)
- Bryant Kim
- Department of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN
46202
| | - Ryan Snyder
- Department of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN
46202
| | - Mulpuri Nagaraju
- Department of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN
46202
| | - Yan Zhou
- Department of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN
46202
| | - Pedro Ojeda-May
- Department of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN
46202
| | - Seth Keeton
- Department of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN
46202
| | - Mellisa Hege
- Department of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN
46202
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of
Oklahoma, 101 Stephenson Pkwy, Norman, OK 73019
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN
46202
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6
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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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7
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Lindsey RK, Bastea S, Goldman N, Fried LE. Investigating 3,4-bis(3-nitrofurazan-4-yl)furoxan detonation with a rapidly tuned density functional tight binding model. J Chem Phys 2021; 154:164115. [PMID: 33940855 DOI: 10.1063/5.0047800] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We describe a machine learning approach to rapidly tune density functional tight binding models for the description of detonation chemistry in organic molecular materials. Resulting models enable simulations on the several 10s of ps scales characteristic to these processes, with "quantum-accuracy." We use this approach to investigate early shock chemistry in 3,4-bis(3-nitrofurazan-4-yl)furoxan, a hydrogen-free energetic material known to form onion-like nanocarbon particulates following detonation. We find that the ensuing chemistry is significantly characterized by the formation of large CxNyOz species, which are likely precursors to the experimentally observed carbon condensates. Beyond utility as a means of investigating detonation chemistry, the present approach can be used to generate quantum-based reference data for the development of full machine-learned interatomic potentials capable of simulation on even greater time and length scales, i.e., for applications where characteristic time scales exceed the reach of methods including Kohn-Sham density functional theory, which are commonly used for reference data generation.
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Affiliation(s)
- Rebecca K Lindsey
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Sorin Bastea
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - 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
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8
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Hamilton BW, Steele BA, Sakano MN, Kroonblawd MP, Kuo IFW, Strachan A. Predicted Reaction Mechanisms, Product Speciation, Kinetics, and Detonation Properties of the Insensitive Explosive 2,6-Diamino-3,5-dinitropyrazine-1-oxide (LLM-105). J Phys Chem A 2021; 125:1766-1777. [PMID: 33617263 DOI: 10.1021/acs.jpca.0c10946] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
2,6-Diamino-3,5-dinitropyrazine-1-oxide (LLM-105) is a relatively new and promising insensitive high-explosive (IHE) material that remains only partially characterized. IHEs are of interest for a range of applications and from a fundamental science standpoint, as the root causes behind insensitivity are poorly understood. We adopt a multitheory approach based on reactive molecular dynamic simulations performed with density functional theory, density functional tight-binding, and reactive force fields to characterize the reaction pathways, product speciation, reaction kinetics, and detonation performance of LLM-105. We compare and contrast these predictions to 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), a prototypical IHE, and 1,3,5,7-tetranitro-1,3,5,7-tetrazoctane (HMX), a more sensitive and higher performance material. The combination of different predictive models allows access to processes operative on progressively longer timescales while providing benchmarks for assessing uncertainties in the predictions. We find that the early reaction pathways of LLM-105 decomposition are extremely similar to TATB; they involve intra- and intermolecular hydrogen transfer. Additionally, the detonation performance of LLM-105 falls between that of TATB and HMX. We find agreement between predictive models for first-step reaction pathways but significant differences in final product formations. Predictions of detonation performance result in a wide range of values, and one-step kinetic parameters show the similar reaction rates at high temperatures for three out of four models considered.
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Affiliation(s)
- Brenden W Hamilton
- School of Materials Engineering and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907, United States
| | - Brad A Steele
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Michael N Sakano
- School of Materials Engineering and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907, United States
| | - Matthew P Kroonblawd
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - I-Feng W Kuo
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Alejandro Strachan
- School of Materials Engineering and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907, United States
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9
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Pham CH, Lindsey RK, Fried LE, Goldman N. Calculation of the detonation state of HN3 with quantum accuracy. J Chem Phys 2020; 153:224102. [DOI: 10.1063/5.0029011] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Cong Huy Pham
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Rebecca K. Lindsey
- 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
| | - Nir Goldman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
- Department of Chemical Engineering, University of California, Davis, California 95616, USA
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10
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Lindsey RK, Goldman N, Fried LE, Bastea S. Many-body reactive force field development for carbon condensation in C/O systems under extreme conditions. J Chem Phys 2020; 153:054103. [DOI: 10.1063/5.0012840] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Rebecca K. Lindsey
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Nir Goldman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
- Department of Chemical Engineering, University of California, Davis, California 95616, USA
| | - Laurence E. Fried
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Sorin Bastea
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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11
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Steele BA, Goldman N, Kuo IFW, Kroonblawd MP. Mechanochemical synthesis of glycine oligomers in a virtual rotational diamond anvil cell. Chem Sci 2020; 11:7760-7771. [PMID: 34123069 PMCID: PMC8163322 DOI: 10.1039/d0sc00755b] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 07/11/2020] [Indexed: 01/18/2023] Open
Abstract
Mechanochemistry of glycine under compression and shear at room temperature is predicted using quantum-based molecular dynamics (QMD) and a simulation design based on rotational diamond anvil cell (RDAC) experiments. Ensembles of high throughput semiempirical density functional tight binding (DFTB) simulations are used to identify chemical trends and bounds for glycine chemistry during rapid shear under compressive loads of up to 15.6 GPa. Significant chemistry is found to occur during compressive shear above 10 GPa. Recovered products consist of small molecules such as water, structural analogs to glycine, heterocyclic molecules, large oligomers, and polypeptides including the simplest polypeptide glycylglycine at up to 4% mass fraction. The population and size of oligomers generally increases with pressure. A number of oligomeric polypeptide precursors and intermediates are also identified that consist of two or three glycine monomers linked together through C-C, C-N, and/or C-O bridges. Even larger oligomers also form that contain peptide C-N bonds and exhibit branched structures. Many of the product molecules exhibit one or more chiral centers. Our simulations demonstrate that athermal mechanical compressive shearing of glycine is a plausible prebiotic route to forming polypeptides.
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Affiliation(s)
- Brad A Steele
- 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
| | - I-Feng W Kuo
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory Livermore CA 94550 USA
| | - Matthew P Kroonblawd
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory Livermore CA 94550 USA
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12
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Dantanarayana V, Nematiaram T, Vong D, Anthony JE, Troisi A, Nguyen Cong K, Goldman N, Faller R, Moulé AJ. Predictive Model of Charge Mobilities in Organic Semiconductor Small Molecules with Force-Matched Potentials. J Chem Theory Comput 2020; 16:3494-3503. [DOI: 10.1021/acs.jctc.0c00211] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Varuni Dantanarayana
- Department of Chemistry, University of California—Davis, Davis, California 95616, United States
- Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Tahereh Nematiaram
- Department of Chemistry and Materials Innovation Factory, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Daniel Vong
- Department of Materials Science and Engineering, University of California—Davis, Davis, California 95616, United States
| | - John E. Anthony
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Alessandro Troisi
- Department of Chemistry and Materials Innovation Factory, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Kien Nguyen Cong
- Department of Physics, University of South Florida, Tampa, Florida 33620, United States
| | - Nir Goldman
- Lawrence Livermore National Laboratory, Livermore, California 94550, United States
- Department of Chemical Engineering, University of California—Davis - Davis, California 95616, United States
| | - Roland Faller
- Department of Chemical Engineering, University of California—Davis - Davis, California 95616, United States
| | - Adam J. Moulé
- Department of Chemical Engineering, University of California—Davis - Davis, California 95616, United States
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13
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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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14
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Cawkwell MJ, Perriot R. Transferable density functional tight binding for carbon, hydrogen, nitrogen, and oxygen: Application to shock compression. J Chem Phys 2019; 150:024107. [DOI: 10.1063/1.5063385] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- M. J. Cawkwell
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - R. Perriot
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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15
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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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16
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Lindsey RK, Fried LE, Goldman N. Application of the ChIMES Force Field to Nonreactive Molecular Systems: Water at Ambient Conditions. J Chem Theory Comput 2018; 15:436-447. [DOI: 10.1021/acs.jctc.8b00831] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- 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
| | - 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
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17
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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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18
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Van den Bossche M, Grönbeck H, Hammer B. Tight-Binding Approximation-Enhanced Global Optimization. J Chem Theory Comput 2018; 14:2797-2807. [DOI: 10.1021/acs.jctc.8b00039] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Maxime Van den Bossche
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
- Science Institute and Faculty of Physical Sciences, University of Iceland, 107 Reykjavík, Iceland
| | - Henrik Grönbeck
- Department of Physics and Competence Centre for Catalysis, Chalmers University of Technology, 412 58 Göteborg, Sweden
| | - Bjørk Hammer
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus, Denmark
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19
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Kroonblawd MP, Pietrucci F, Saitta AM, Goldman N. Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model. J Chem Theory Comput 2018. [PMID: 29543444 DOI: 10.1021/acs.jctc.7b01266] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTB model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol-1.
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Affiliation(s)
- Matthew P Kroonblawd
- Physical and Life Sciences Directorate , Lawrence Livermore National Laboratory , Livermore , California 94550 , United States
| | - Fabio Pietrucci
- Sorbonne Université, Muséum National d'Histoire Naturelle , UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC , F-75005 Paris , France
| | - Antonino Marco Saitta
- Sorbonne Université, Muséum National d'Histoire Naturelle , UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC , F-75005 Paris , France
| | - 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
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20
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Trnka T, Tvaroška I, Koča J. Automated Training of ReaxFF Reactive Force Fields for Energetics of Enzymatic Reactions. J Chem Theory Comput 2017; 14:291-302. [DOI: 10.1021/acs.jctc.7b00870] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Igor Tvaroška
- Institute
of Chemistry, Slovak Academy of Sciences, 845 38 Bratislava, Slovak Republic
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21
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Lindsey RK, Fried LE, Goldman N. ChIMES: A Force Matched Potential with Explicit Three-Body Interactions for Molten Carbon. J Chem Theory Comput 2017; 13:6222-6229. [DOI: 10.1021/acs.jctc.7b00867] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- 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
| | - Nir Goldman
- Physical and Life Sciences
Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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22
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Krishnapriyan A, Yang P, Niklasson AMN, Cawkwell MJ. Numerical Optimization of Density Functional Tight Binding Models: Application to Molecules Containing Carbon, Hydrogen, Nitrogen, and Oxygen. J Chem Theory Comput 2017; 13:6191-6200. [DOI: 10.1021/acs.jctc.7b00762] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A. Krishnapriyan
- Department
of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
- Theoretical
Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - P. Yang
- Theoretical
Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - A. M. N. Niklasson
- Theoretical
Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - M. J. Cawkwell
- Theoretical
Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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23
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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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