1
|
Spencer RJ, Zhanserkeev AA, Yang EL, Steele RP. The Near-Sightedness of Many-Body Interactions in Anharmonic Vibrational Couplings. J Am Chem Soc 2024; 146:15376-15392. [PMID: 38771156 DOI: 10.1021/jacs.4c03198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Couplings between vibrational motions are driven by electronic interactions, and these couplings carry special significance in vibrational energy transfer, multidimensional spectroscopy experiments, and simulations of vibrational spectra. In this investigation, the many-body contributions to these couplings are analyzed computationally in the context of clathrate-like alkali metal cation hydrates, including Cs+(H2O)20, Rb+(H2O)20, and K+(H2O)20, using both analytic and quantum-chemistry potential energy surfaces. Although the harmonic spectra and one-dimensional anharmonic spectra depend strongly on these many-body interactions, the mode-pair couplings were, perhaps surprisingly, found to be dominated by one-body effects, even in cases of couplings to low-frequency modes that involved the motion of multiple water molecules. The origin of this effect was traced mainly to geometric distortion within water monomers and cancellation of many-body effects in differential couplings, and the effect was also shown to be agnostic to the identity of the ion. These outcomes provide new understanding of vibrational couplings and suggest the possibility of improved computational methods for the simulation of infrared and Raman spectra.
Collapse
Affiliation(s)
- Ryan J Spencer
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Asylbek A Zhanserkeev
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Emily L Yang
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| |
Collapse
|
2
|
Houston PL, Qu C, Yu Q, Pandey P, Conte R, Nandi A, Bowman JM. No Headache for PIPs: A PIP Potential for Aspirin Runs Much Faster and with Similar Precision Than Other Machine-Learned Potentials. J Chem Theory Comput 2024; 20:3008-3018. [PMID: 38593438 DOI: 10.1021/acs.jctc.4c00054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Assessments of machine-learning (ML) potentials are an important aspect of the rapid development of this field. We recently reported an assessment of the linear-regression permutationally invariant polynomial (PIP) method for ethanol, using the widely used (revised) rMD17 data set. We demonstrated that the PIP approach outperformed numerous other methods, e.g., ANI, PhysNet, sGDML, and p-KRR, with respect to precision and notably with respect to speed [Houston et al., J. Chem. Phys. 2022, 156, 044120]. Here, we extend this assessment to the 21-atom aspirin molecule, using the rMD17 data set, with a focus on the speed of evaluation. Both energies and forces are used for training, and the precision of several PIPs is examined for both. Normal mode frequencies, the methyl torsional potential, and 1d vibrational energies for an OH stretch are presented. We show that the PIP approach achieves the level of precision obtained from other ML methods, e.g., atom-centered neural network methods, linear regression ACE, and kernel methods, as reported by Kovács et al. in J. Chem. Theory Comput. 2021, 17, 7696-7711. More significantly, we show that the PIP PESs run much faster than all other ML methods, whose timings were evaluated in that paper. We also show that the PIP PES extrapolates well enough to describe several internal motions of aspirin, including an OH stretch.
Collapse
Affiliation(s)
- Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Chen Qu
- Independent Researcher, Toronto, Ontario M9B0E3, Canada
| | - Qi Yu
- Department of Chemistry, Fudan University, Shanghai 200438, P. R. China
| | - Priyanka Pandey
- Department of Chemistry, Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Apurba Nandi
- Department of Chemistry, Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
- Department of Physics and Materials Science, University of Luxembourg, Luxembourg City L-1511, Luxembourg
| | - Joel M Bowman
- Department of Chemistry, Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
3
|
Lambros E, Fetherolf JH, Hammes-Schiffer S, Li X. A Many-Body Perspective of Nuclear Quantum Effects in Aqueous Clusters. J Phys Chem Lett 2024; 15:4070-4075. [PMID: 38587257 DOI: 10.1021/acs.jpclett.4c00439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Nuclear quantum effects play an important role in the structure and thermodynamics of aqueous systems. By performing a many-body expansion with nuclear-electronic orbital (NEO) theory, we show that proton quantization can give rise to significant energetic contributions for many-body interactions spanning several molecules in single-point energy calculations of water clusters. Although zero-point motion produces a large increase in energy at the one-body level, nuclear quantum effects serve to stabilize higher-order molecular interactions. These results are significant because they demonstrate that nuclear quantum effects play a nontrivial role in many-body interactions of aqueous systems. Our approach also provides a pathway for incorporating nuclear quantum effects into water potential energy surfaces. The NEO approach is advantageous for many-body expansion analyses because it includes nuclear quantum effects directly in the energies.
Collapse
Affiliation(s)
- Eleftherios Lambros
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Jonathan H Fetherolf
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
4
|
Zhai Y, Rashmi R, Palos E, Paesani F. Many-body interactions and deep neural network potentials for water. J Chem Phys 2024; 160:144501. [PMID: 38587225 DOI: 10.1063/5.0203682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/23/2024] [Indexed: 04/09/2024] Open
Abstract
We present a detailed assessment of deep neural network potentials developed within the Deep Potential Molecular Dynamics (DeePMD) framework and trained on the MB-pol data-driven many-body potential energy function. Specific focus is directed at the ability of DeePMD-based potentials to correctly reproduce the accuracy of MB-pol across various water systems. Analyses of bulk and interfacial properties as well as many-body interactions characteristic of water elucidate inherent limitations in the transferability and predictive accuracy of DeePMD-based potentials. These limitations can be traced back to an incomplete implementation of the "nearsightedness of electronic matter" principle, which may be common throughout machine learning potentials that do not include a proper representation of self-consistently determined long-range electric fields. These findings provide further support for the "short-blanket dilemma" faced by DeePMD-based potentials, highlighting the challenges in achieving a balance between computational efficiency and a rigorous, physics-based representation of the properties of water. Finally, we believe that our study contributes to the ongoing discourse on the development and application of machine learning models in simulating water systems, offering insights that could guide future improvements in the field.
Collapse
Affiliation(s)
- Yaoguang Zhai
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
| | - Richa Rashmi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Etienne Palos
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
- Halicioğlu Data Science Institute, University of California San Diego, La Jolla, California 92093, USA
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, USA
| |
Collapse
|
5
|
Arandhara M, Ramesh SG. Nuclear Quantum Effects in Hydroxide Hydrate Along the H-Bond Bifurcation Pathway. J Phys Chem A 2024; 128:1600-1610. [PMID: 38393819 DOI: 10.1021/acs.jpca.3c08027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Path integral (PI) simulations are used to explore nuclear quantum effects (NQEs) in hydroxide hydrate and its perdeuterated isotopomer along the H-bond bifurcation pathway. Toward this, a new potential energy surface using the symmetric gradient domain machine learning method with ab initio data at the CCSD(T)/aug-cc-pVTZ level is built. From PI umbrella sampling (US) simulations, free energy profiles along the bifurcation coordinate are explored as a function of temperature. At ambient temperature, the bifurcation barrier is increased upon inclusion of NQEs. At low temperatures in the deep tunneling regime, the barrier is strongly decreased and flattened. These trends are examined, and the role of the O-O distance is also investigated through two-dimensional US simulations.
Collapse
Affiliation(s)
- Mrinal Arandhara
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sai G Ramesh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
6
|
Savoj R, Agnew H, Zhou R, Paesani F. Molecular Insights into the Influence of Ions on the Water Structure. I. Alkali Metal Ions in Solution. J Phys Chem B 2024; 128:1953-1962. [PMID: 38373140 DOI: 10.1021/acs.jpcb.3c08150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
In this study, we explore the impact of alkali metal ions (Li+, Na+, K+, Rb+, and Cs+) on the hydration structure of water using molecular dynamics simulations carried out with MB-nrg potential energy functions (PEFs). Our analyses include radial distribution functions, coordination numbers, dipole moments, and infrared spectra of water molecules, calculated as a function of solvation shells. The results collectively indicate a highly local influence of all of the alkali metal ions on the hydrogen-bond network established by the surrounding water molecules, with the smallest and most densely charged Li+ ion exerting the most pronounced effect. Remarkably, the MB-nrg PEFs demonstrate excellent agreement with available experimental data for the position and size of the first solvation shells, underscoring their potential as predictive models for realistic simulations of ionic aqueous solutions across various thermodynamic conditions and environments.
Collapse
Affiliation(s)
- Roya Savoj
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Henry Agnew
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Ruihan Zhou
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, 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
- Halicioğlu Data Science Institute, 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
|
7
|
Chen J, Yu K. PhyNEO: A Neural-Network-Enhanced Physics-Driven Force Field Development Workflow for Bulk Organic Molecule and Polymer Simulations. J Chem Theory Comput 2024; 20:253-265. [PMID: 38118076 DOI: 10.1021/acs.jctc.3c01045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
An accurate, generalizable, and transferable force field plays a crucial role in the molecular dynamics simulations of organic polymers and biomolecules. Conventional empirical force fields often fail to capture precise intermolecular interactions due to their negligence of important physics, such as polarization, charge penetration, many-body dispersion, etc. Moreover, the parameterization of these force fields relies heavily on top-down fittings, limiting their transferabilities to new systems where the experimental data are often unavailable. To address these challenges, we introduce a general and fully ab initio force field construction strategy, named PhyNEO. It features a hybrid approach that combines both the physics-driven and the data-driven methods and is able to generate a bulk potential with chemical accuracy using only quantum chemistry data of very small clusters. Careful separations of long-/short-range interactions and nonbonding/bonding interactions are the key to the success of PhyNEO. By such a strategy, we mitigate the limitations of pure data-driven methods in long-range interactions, thus largely increasing the data efficiency and the scalability of machine learning models. The new approach is thoroughly tested on poly(ethylene oxide) and polyethylene glycol systems, giving superior accuracies in both microscopic and bulk properties compared to conventional force fields. This work thus offers a promising framework for the development of advanced force fields in a wide range of organic molecular systems.
Collapse
Affiliation(s)
- Junmin Chen
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, Guangdong 518055, P. R. China
| | - Kuang Yu
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, Guangdong 518055, P. R. China
- Institute of Materials Research (iMR), Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong 518055, P. R. China
| |
Collapse
|
8
|
Yang EL, Talbot JJ, Spencer RJ, Steele RP. Pitfalls in the n-mode representation of vibrational potentials. J Chem Phys 2023; 159:204104. [PMID: 38010326 DOI: 10.1063/5.0176612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/19/2023] [Indexed: 11/29/2023] Open
Abstract
Simulations of anharmonic vibrational motion rely on computationally expedient representations of the governing potential energy surface. The n-mode representation (n-MR)-effectively a many-body expansion in the space of molecular vibrations-is a general and efficient approach that is often used for this purpose in vibrational self-consistent field (VSCF) calculations and correlated analogues thereof. In the present analysis, a lack of convergence in many VSCF calculations is shown to originate from negative and unbound potentials at truncated orders of the n-MR expansion. For cases of strong anharmonic coupling between modes, the n-MR can both dip below the true global minimum of the potential surface and lead to effective single-mode potentials in VSCF that do not correspond to bound vibrational problems, even for bound total potentials. The present analysis serves mainly as a pathology report of this issue. Furthermore, this insight into the origin of VSCF non-convergence provides a simple, albeit ad hoc, route to correct the problem by "painting in" the full representation of groups of modes that exhibit these negative potentials at little additional computational cost. Somewhat surprisingly, this approach also reasonably approximates the results of the next-higher n-MR order and identifies groups of modes with particularly strong coupling. The method is shown to identify and correct problematic triples of modes-and restore SCF convergence-in two-mode representations of challenging test systems, including the water dimer and trimer, as well as protonated tropine.
Collapse
Affiliation(s)
- Emily L Yang
- Department of Chemistry, The University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
- Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
| | - Justin J Talbot
- Department of Chemistry, University of California-Berkeley, 420 Latimer Hall, Berkeley, California 94720, USA
| | - Ryan J Spencer
- Department of Chemistry, The University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
- Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
| | - Ryan P Steele
- Department of Chemistry, The University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
- Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
| |
Collapse
|
9
|
Zhanserkeev AA, Yang EL, Steele RP. Accelerating Anharmonic Spectroscopy Simulations via Local-Mode, Multilevel Methods. J Chem Theory Comput 2023; 19:5572-5585. [PMID: 37555634 DOI: 10.1021/acs.jctc.3c00589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Ab initio computer simulations of anharmonic vibrational spectra provide nuanced insight into the vibrational behavior of molecules and complexes. The computational bottleneck in such simulations, particularly for ab initio potentials, is often the generation of mode-coupling potentials. Focusing specifically on two-mode couplings in this analysis, the combination of a local-mode representation and multilevel methods is demonstrated to be particularly symbiotic. In this approach, a low-level quantum chemistry method is employed to predict the pairwise couplings that should be included at the target level of theory in vibrational self-consistent field (and similar) calculations. Pairs that are excluded by this approach are "recycled" at the low level of theory. Furthermore, because this low-level pre-screening will eventually become the computational bottleneck for sufficiently large chemical systems, distance-based truncation is applied to these low-level predictions without substantive loss of accuracy. This combination is demonstrated to yield sub-wavenumber fidelity with reference vibrational transitions when including only a small fraction of target-level couplings; the overhead of predicting these couplings, particularly when employing distance-based, local-mode cutoffs, is a trivial added cost. This combined approach is assessed on a series of test cases, including ethylene, hexatriene, and the alanine dipeptide. Vibrational self-consistent field (VSCF) spectra were obtained with an RI-MP2/cc-pVTZ potential for the dipeptide, at approximately a 5-fold reduction in computational cost. Considerable optimism for increased accelerations for larger systems and higher-order couplings is also justified, based on this investigation.
Collapse
Affiliation(s)
- Asylbek A Zhanserkeev
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Emily L Yang
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| |
Collapse
|
10
|
Riera M, Knight C, Bull-Vulpe EF, Zhu X, Agnew H, Smith DGA, Simmonett AC, Paesani F. MBX: A many-body energy and force calculator for data-driven many-body simulations. J Chem Phys 2023; 159:054802. [PMID: 37526156 PMCID: PMC10550339 DOI: 10.1063/5.0156036] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/11/2023] [Indexed: 08/02/2023] Open
Abstract
Many-Body eXpansion (MBX) is a C++ library that implements many-body potential energy functions (PEFs) within the "many-body energy" (MB-nrg) formalism. MB-nrg PEFs integrate an underlying polarizable model with explicit machine-learned representations of many-body interactions to achieve chemical accuracy from the gas to the condensed phases. MBX can be employed either as a stand-alone package or as an energy/force engine that can be integrated with generic software for molecular dynamics and Monte Carlo simulations. MBX is parallelized internally using Open Multi-Processing and can utilize Message Passing Interface when available in interfaced molecular simulation software. MBX enables classical and quantum molecular simulations with MB-nrg PEFs, as well as hybrid simulations that combine conventional force fields and MB-nrg PEFs, for diverse systems ranging from small gas-phase clusters to aqueous solutions and molecular fluids to biomolecular systems and metal-organic frameworks.
Collapse
Affiliation(s)
- Marc Riera
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Christopher Knight
- Argonne National Laboratory, Computational Science Division, Lemont, Illinois 60439, USA
| | - Ethan F. Bull-Vulpe
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Xuanyu Zhu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Henry Agnew
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | | | - Andrew C. Simmonett
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | |
Collapse
|
11
|
Bore SL, Paesani F. Realistic phase diagram of water from "first principles" data-driven quantum simulations. Nat Commun 2023; 14:3349. [PMID: 37291095 DOI: 10.1038/s41467-023-38855-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/12/2023] [Indexed: 06/10/2023] Open
Abstract
Since the experimental characterization of the low-pressure region of water's phase diagram in the early 1900s, scientists have been on a quest to understand the thermodynamic stability of ice polymorphs on the molecular level. In this study, we demonstrate that combining the MB-pol data-driven many-body potential for water, which was rigorously derived from "first principles" and exhibits chemical accuracy, with advanced enhanced-sampling algorithms, which correctly describe the quantum nature of molecular motion and thermodynamic equilibria, enables computer simulations of water's phase diagram with an unprecedented level of realism. Besides providing fundamental insights into how enthalpic, entropic, and nuclear quantum effects shape the free-energy landscape of water, we demonstrate that recent progress in "first principles" data-driven simulations, which rigorously encode many-body molecular interactions, has opened the door to realistic computational studies of complex molecular systems, bridging the gap between experiments and simulations.
Collapse
Affiliation(s)
- Sigbjørn Løland Bore
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, 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.
- Halicioğlu Data Science Institute, 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
|