1
|
Iyengar SS, Schlegel HB, Sumner I, Li J. Rare Events Sampling Methods for Quantum and Classical Ab Initio Molecular Dynamics. J Phys Chem A 2024; 128:5386-5397. [PMID: 38951489 DOI: 10.1021/acs.jpca.3c07385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
We provide an approach to sample rare events during classical ab initio molecular dynamics and quantum wavepacket dynamics. For classical AIMD, a set of fictitious degrees of freedom are introduced that may harmonically interact with the electronic and nuclear degrees of freedom to steer the dynamics in a conservative fashion toward energetically forbidden regions. A similar approach when introduced for quantum wavepacket dynamics has the effect of biasing the trajectory of the wavepacket centroid toward the regions of the potential surface that are difficult to sample. The approach is demonstrated for a phenol-amine system, which is a prototypical problem for condensed phase-proton transfer, and for model potentials undergoing wavepacket dynamics. In all cases, the approach yields trajectories that conserve energy while sampling rare events.
Collapse
Affiliation(s)
- Srinivasan S Iyengar
- Department of Chemistry, Department of Physics, and the Indiana University Quantum Science and Engineering Center (IU-QSEC), Indiana University, 800 E. Kirkwood Avenue, Bloomington 47405, Indiana, United States
| | - H Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit 48202, Michigan, United States
| | - Isaiah Sumner
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg 22807, Virginia, United States
| | - Junjie Li
- Texas Advanced Computing Center, The University of Texas at Austin, Austin 78758, Texas, United States
| |
Collapse
|
2
|
Ricard TC, Zhu X, Iyengar SS. Capturing Weak Interactions in Surface Adsorbate Systems at Coupled Cluster Accuracy: A Graph-Theoretic Molecular Fragmentation Approach Improved through Machine Learning. J Chem Theory Comput 2023. [PMID: 38019639 DOI: 10.1021/acs.jctc.3c00955] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
The accurate and efficient study of the interactions of organic matter with the surface of water is critical to a wide range of applications. For example, environmental studies have found that acidic polyfluorinated alkyl substances, especially perfluorooctanoic acid (PFOA), have spread throughout the environment and bioaccumulate into human populations residing near contaminated watersheds, leading to many systemic maladies. Thus, the study of the interactions of PFOA with water surfaces became important for the mitigation of their activity as pollutants and threats to public health. However, theoretical study of the interactions of such organic adsorbates on the surface of water, and their bulk concerted properties, often necessitates the use of ab initio methods to properly incorporate the long-range electronic properties that govern these extended systems. Notable theoretical treatments of "on-water" reactions thus far have employed hybrid DFT and semilocal DFT, but the interactions involved are weak interactions that may be best described using post-Hartree-Fock theory. Here, we aim to demonstrate the utility of a graph-theoretic approach to molecular fragmentation that accurately captures the critical "weak" interactions while maintaining an efficient ab initio treatment of the long-range periodic interactions that underpin the physics of extended systems. We apply this graph-theoretical treatment to study PFOA on the surface of water as a model system for the study of weak interactions seen in the wide range of surface interactions and reactions. The approach divides a system into a set of vertices, that are then connected through edges, faces, and higher order graph theoretic objects known as simplexes, to represent a collection of locally interacting subsystems. These subsystems are then used to construct ab initio molecular dynamics simulations and for computing multidimensional potential energy surfaces. To further improve the computational efficiency of our graph theoretic fragmentation method, we use a recently developed transfer learning protocol to construct the full system potential energy from a family of neural networks each designed to accurately model the behavior of individual simplexes. We use a unique multidimensional clustering algorithm, based on the k-means clustering methodology, to define our training space for each separate simplex. These models are used to extrapolate the energies for molecular dynamics trajectories at PFOA water interfaces, at less than one-tenth the cost as compared to a regular molecular fragmentation-based dynamics calculation with excellent agreement with couple cluster level of full system potential energies.
Collapse
Affiliation(s)
- Timothy C Ricard
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Xiao Zhu
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| |
Collapse
|
3
|
Ricard TC, Iyengar SS. Efficient and Accurate Approach To Estimate Hybrid Functional and Large Basis-Set Contributions to Condensed-Phase Systems and Molecule–Surface Interactions. J Chem Theory Comput 2020; 16:4790-4812. [DOI: 10.1021/acs.jctc.9b01089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Timothy C. Ricard
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| |
Collapse
|
4
|
Saller MAC, Habershon S. Quantum Dynamics with Short-Time Trajectories and Minimal Adaptive Basis Sets. J Chem Theory Comput 2017; 13:3085-3096. [DOI: 10.1021/acs.jctc.7b00021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maximilian A. C. Saller
- Department of Chemistry and
Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Scott Habershon
- Department of Chemistry and
Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, United Kingdom
| |
Collapse
|
5
|
Brela MZ, Boczar M, Wójcik MJ, Sato H, Nakajima T, Ozaki Y. The Born-Oppenheimer molecular simulations of infrared spectra of crystalline poly-(R)-3-hydroxybutyrate with analysis of weak C H⋯O C hydrogen bonds. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.04.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
6
|
Hirshberg B, Gerber RB. Mean-Field Methods for Time-Dependent Quantum Dynamics of Many-Atom Systems. ADVANCES IN QUANTUM CHEMISTRY 2017. [DOI: 10.1016/bs.aiq.2017.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
7
|
Brela MZ, Wójcik MJ, Witek ŁJ, Boczar M, Wrona E, Hashim R, Ozaki Y. Born-Oppenheimer Molecular Dynamics Study on Proton Dynamics of Strong Hydrogen Bonds in Aspirin Crystals, with Emphasis on Differences between Two Crystal Forms. J Phys Chem B 2016; 120:3854-62. [PMID: 27045959 DOI: 10.1021/acs.jpcb.6b01601] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, the proton dynamics of hydrogen bonds for two forms of crystalline aspirin was investigated by the Born-Oppenheimer molecular dynamics (BOMD) method. Analysis of the geometrical parameters of hydrogen bonds using BOMD reveals significant differences in hydrogen bonding between the two crystalline forms of aspirin, Form I and Form II. Analysis of the trajectory for Form I shows spontaneous proton transfer in cyclic dimers, which is absent in Form II. Quantization of the O-H stretching modes allows a detailed discussion on the strength of hydrogen-bonding interactions. The focal point of our study is examination of the hydrogen bond characteristics in the crystal structure and clarification of the influence of hydrogen bonding on the presence of the two crystalline forms of aspirin. In the BOMD method, thermal motions were taken into account. Solving the Schrödinger equation for the snapshots of 2D proton potentials, extracted from MD, gives the best agreement with IR spectra. The character of medium-strong hydrogen bonds in Form I of aspirin was compared with that of weaker hydrogen bonds in aspirin Form II. Two proton minima are present in the potential function for the hydrogen bonds in Form I. The band contours, calculated by using one- and two-dimensional O-H quantization, reflect the differences in the hydrogen bond strengths between the two crystalline forms of aspirin, as well as the strong hydrogen bonding in the cyclic dimers of Form I and the medium-strong hydrogen bonding in Form II.
Collapse
Affiliation(s)
- Mateusz Z Brela
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland
| | - Marek J Wójcik
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland
| | - Łukasz J Witek
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland
| | - Marek Boczar
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland
| | - Ewa Wrona
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland
| | - Rauzah Hashim
- Department of Chemistry, University of Malaya , 50603 Kuala Lumpur, Malaysia
| | - Yukihiro Ozaki
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University , Sanda, Hyogo 669-1337, Japan
| |
Collapse
|
8
|
Brela MZ, Wójcik MJ, Boczar M, Witek Ł, Yasuda M, Ozaki Y. Car–Parrinello Molecular Dynamics Simulations of Infrared Spectra of Crystalline Vitamin C with Analysis of Double Minimum Proton Potentials for Medium-Strong Hydrogen Bonds. J Phys Chem B 2015; 119:7922-30. [DOI: 10.1021/acs.jpcb.5b02777] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Mateusz Z. Brela
- Research
Group of Molecular Modelling of Catalytic Processes, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Marek J. Wójcik
- Laboratory
of Molecular Spectroscopy, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Marek Boczar
- Laboratory
of Molecular Spectroscopy, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Łukasz Witek
- Photochemistry
and Luminescence Research Group, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Mitsuru Yasuda
- Department
of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
| | - Yukihiro Ozaki
- Department
of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
| |
Collapse
|
9
|
Prociuk AH, Iyengar SS. A Multiwavelet Treatment of the Quantum Subsystem in Quantum Wavepacket Ab Initio Molecular Dynamics through an Hierarchical Partitioning of Momentum Space. J Chem Theory Comput 2014; 10:2950-63. [DOI: 10.1021/ct5003016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexander H. Prociuk
- Department of Chemistry and
Department of Physics, Indiana University, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and
Department of Physics, Indiana University, Bloomington, Indiana 47405, United States
| |
Collapse
|
10
|
Li J, Li X, Iyengar SS. Vibrational Properties of Hydrogen-Bonded Systems Using the Multireference Generalization to the “On-the-Fly” Electronic Structure within Quantum Wavepacket ab Initio Molecular Dynamics (QWAIMD). J Chem Theory Comput 2014; 10:2265-80. [DOI: 10.1021/ct5002347] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Junjie Li
- Department of Chemistry and
Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Xiaohu Li
- Department of Chemistry and
Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and
Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| |
Collapse
|
11
|
Dietrick SM, Iyengar SS. Constructing Periodic Phase Space Orbits from ab Initio Molecular Dynamics Trajectories to Analyze Vibrational Spectra: Case Study of the Zundel (H5O2+) Cation. J Chem Theory Comput 2012; 8:4876-90. [DOI: 10.1021/ct300695x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Scott M. Dietrick
- Department
of Chemistry and Department of Physics, Indiana University, Bloomington, Indiana
47405, United States
| | - Srinivasan S. Iyengar
- Department
of Chemistry and Department of Physics, Indiana University, Bloomington, Indiana
47405, United States
| |
Collapse
|
12
|
Brela M, Stare J, Pirc G, Sollner-Dolenc M, Boczar M, Wójcik MJ, Mavri J. Car-Parrinello simulation of the vibrational spectrum of a medium strong hydrogen bond by two-dimensional quantization of the nuclear motion: application to 2-hydroxy-5-nitrobenzamide. J Phys Chem B 2012; 116:4510-8. [PMID: 22429110 DOI: 10.1021/jp2094559] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The nature of medium strong intra- and intermolecular hydrogen bonding in 2-hydroxy-5-nitrobenzamide in the crystal phase was examined by infrared spectroscopy and Car-Parrinello molecular dynamics simulation. The focal point of our study was the part of the infrared spectra associated with the O-H and N-H stretching modes that are very sensitive to the strength of hydrogen bonding. For spectra calculations we used an isolated dimer and the fully periodic crystal environment. We calculated the spectra by using harmonic approximation, the time course of the dipole moment function as obtained from the Car-Parrinello simulation, and the quantization of the nuclear motion of the proton for an instantaneous snapshot of the structures in one and two dimensions. Although quantitative assessment of the agreement between the computed and experimental band contour is difficult due to the fact that the experimental band is very broad, we feel that the most reasonable qualitative agreement with the experiment is obtained from snapshot structures and two-dimensional quantization of the proton motion. We have also critically examined the methods of constructing the one-dimensional proton potential. Perspectives are given for the treatment of nuclear quantum effects in biocatalysis.
Collapse
Affiliation(s)
- Mateusz Brela
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Ljubljana, Slovenia
| | | | | | | | | | | | | |
Collapse
|
13
|
Xia J, Huang C, Shin I, Carter EA. Can orbital-free density functional theory simulate molecules? J Chem Phys 2012; 136:084102. [DOI: 10.1063/1.3685604] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
14
|
Dietrick SM, Pacheco AB, Phatak P, Stevens PS, Iyengar SS. Influence of Water on Anharmonicity, Stability, and Vibrational Energy Distribution of Hydrogen-Bonded Adducts in Atmospheric Reactions: Case Study of the OH + Isoprene Reaction Intermediate Using Ab Initio Molecular Dynamics. J Phys Chem A 2011; 116:399-414. [DOI: 10.1021/jp204511v] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Scott M. Dietrick
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Alexander B. Pacheco
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Prasad Phatak
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Philip S. Stevens
- Department of Chemistry and Center for Research in Environmental Science, School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Departments of Chemistry and Physics, Indiana University, Bloomington, Indiana 47405, United States
| |
Collapse
|