1
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Sattasathuchana T, Xu P, Bertoni C, Kim YL, Leang SS, Pham BQ, Gordon MS. The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems. J Chem Theory Comput 2024; 20:2445-2461. [PMID: 38450638 DOI: 10.1021/acs.jctc.3c01309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
The effective fragment molecular orbital (EFMO) method has been developed to predict the total energy of a very large molecular system accurately (with respect to the underlying quantum mechanical method) and efficiently by taking advantage of the locality of strong chemical interactions and employing a two-level hierarchical parallelism. The accuracy of the EFMO method is partly attributed to the accurate and robust intermolecular interaction prediction between distant fragments, in particular, the many-body polarization and dispersion effects, which require the generation of static and dynamic polarizability tensors by solving the coupled perturbed Hartree-Fock (CPHF) and time-dependent HF (TDHF) equations, respectively. Solving the CPHF and TDHF equations is the main EFMO computational bottleneck due to the inefficient (serial) and I/O-intensive implementation of the CPHF and TDHF solvers. In this work, the efficiency and scalability of the EFMO method are significantly improved with a new CPU memory-based implementation for solving the CPHF and TDHF equations that are parallelized by either message passing interface (MPI) or hybrid MPI/OpenMP. The accuracy of the EFMO method is demonstrated for both covalently bonded systems and noncovalently bound molecular clusters by systematically examining the effects of basis sets and a key distance-related cutoff parameter, Rcut. Rcut determines whether a fragment pair (dimer) is treated by the chosen ab initio method or calculated using the effective fragment potential (EFP) method (separated dimers). Decreasing the value of Rcut increases the number of separated (EFP) dimers, thereby decreasing the computational effort. It is demonstrated that excellent accuracy (<1 kcal/mol error per fragment) can be achieved when using a sufficiently large basis set with diffuse functions coupled with a small Rcut value. With the new parallel implementation, the total EFMO wall time is substantially reduced, especially with a high number of MPI ranks. Given a sufficient workload, nearly ideal strong scaling is achieved for the CPHF and TDHF parts of the calculation. For the first time, EFMO calculations with the inclusion of long-range polarization and dispersion interactions on a hydrated mesoporous silica nanoparticle with explicit water solvent molecules (more than 15k atoms) are achieved on a massively parallel supercomputer using nearly 1000 physical nodes. In addition, EFMO calculations on the carbinolamine formation step of an amine-catalyzed aldol reaction at the nanoscale with explicit solvent effects are presented.
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Affiliation(s)
- Tosaporn Sattasathuchana
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50011, United States
| | - Peng Xu
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50011, United States
| | - Colleen Bertoni
- Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Yu Lim Kim
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Sarom S Leang
- EP Analytics, Inc., 9909 Mira Mesa Blvd Ste. 230, San Diego, California 92131, United States
| | - Buu Q Pham
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50011, United States
| | - Mark S Gordon
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50011, United States
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2
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Xu P, Leonard SL, O'Brien W, Gordon MS. R -8 Dispersion Interaction: Derivation and Application to the Effective Fragment Potential Method. J Phys Chem A 2024; 128:292-327. [PMID: 38150458 DOI: 10.1021/acs.jpca.3c05115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
The anisotropic and isotropic R-8 dispersion contributions (disp8) are derived and implemented within the framework of the effective fragment potential (EFP) method formulated with imaginary frequency-dependent Cartesian polarizability tensors distributed at the centroids of the localized molecular orbitals (LMOs). Two forms of damping functions, intermolecular overlap-based and Tang-Toennies, are extended for disp8. To obtain LMO polarizability tensors centered at LMO centroids, an origin-shifting transformation is derived and implemented for the dipole-octopole polarizability tensor and the quadrupole-quadrupole polarizability tensor. The analytic gradient is derived and implemented for the isotropic disp8 contribution. Relative to the previously implemented empirical EFP disp8 energy, the isotropic disp8 component of the interaction energy improves the overall agreement of the EFP dispersion energies with the symmetry-adapted perturbation theory (SAPT) benchmarks, reducing the mean absolute errors (MAEs) and mean absolute percentage errors for most of the databases examined in this work. While the anisotropic disp8 can further enhance the accuracy of the EFP dispersion energy and yield smaller MAEs, significantly overbound dispersion energies are predicted by the anisotropic disp8 when the maximum element in the intermolecular overlap matrix is greater than 0.1, possibly due to the breakdown of the approximations made in the EFP dispersion derivation at a short range. For potential energy scan databases, the newly developed EFP dispersion model with isotropic disp8 yields the overall correct curvature and good agreement with SAPT benchmarks around equilibrium and longer but overestimates the dispersion interactions at a short range. While the overlap-based dispersion-damping functions produce better MAEs than Tang-Toennies damping functions, further improvement is needed to better screen the large attractive dispersion energies at a short range (overlap >0.1).
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Affiliation(s)
- Peng Xu
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50014, United States
| | - Samuel L Leonard
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50014, United States
| | - William O'Brien
- Science Undergraduate Research Internship (SULI): Department of Energy, Ames National Laboratory, Iowa State University, Ames, Iowa50011-3020, United States
| | - Mark S Gordon
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50014, United States
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3
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Zahariev F, Xu P, Westheimer BM, Webb S, Galvez Vallejo J, Tiwari A, Sundriyal V, Sosonkina M, Shen J, Schoendorff G, Schlinsog M, Sattasathuchana T, Ruedenberg K, Roskop LB, Rendell AP, Poole D, Piecuch P, Pham BQ, Mironov V, Mato J, Leonard S, Leang SS, Ivanic J, Hayes J, Harville T, Gururangan K, Guidez E, Gerasimov IS, Friedl C, Ferreras KN, Elliott G, Datta D, Cruz DDA, Carrington L, Bertoni C, Barca GMJ, Alkan M, Gordon MS. The General Atomic and Molecular Electronic Structure System (GAMESS): Novel Methods on Novel Architectures. J Chem Theory Comput 2023; 19:7031-7055. [PMID: 37793073 DOI: 10.1021/acs.jctc.3c00379] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
The primary focus of GAMESS over the last 5 years has been the development of new high-performance codes that are able to take effective and efficient advantage of the most advanced computer architectures, both CPU and accelerators. These efforts include employing density fitting and fragmentation methods to reduce the high scaling of well-correlated (e.g., coupled-cluster) methods as well as developing novel codes that can take optimal advantage of graphical processing units and other modern accelerators. Because accurate wave functions can be very complex, an important new functionality in GAMESS is the quasi-atomic orbital analysis, an unbiased approach to the understanding of covalent bonds embedded in the wave function. Best practices for the maintenance and distribution of GAMESS are also discussed.
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Affiliation(s)
- Federico Zahariev
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Peng Xu
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Bryce M Westheimer
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Simon Webb
- VeraChem LLC, 12850 Middlebrook Road, Suite 205, Germantown, Maryland 20874-5244, United States
| | - Jorge Galvez Vallejo
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
- Research School of Computer Science, Australian National University, Canberra, ACT 2601, Australia
| | - Ananta Tiwari
- EP Analytics, Inc., 9909 Mira Mesa Boulevard, Suite 230, San Diego, California 92131, United States
| | - Vaibhav Sundriyal
- Department of Computational Modeling and Simulation Engineering, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Masha Sosonkina
- Department of Computational Modeling and Simulation Engineering, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Jun Shen
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - George Schoendorff
- Propellants Branch, Rocket Propulsion Division, Aerospace Systems Directorate, Air Force Research Laboratory, AFRL/RQRP, Edwards Air Force Base, California 93524, United States
| | - Megan Schlinsog
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Tosaporn Sattasathuchana
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Klaus Ruedenberg
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Luke B Roskop
- Hewlett-Packard Enterprise, 2131 Lindau Lane #1000, Bloomington, Minnesota 55425, United States
| | | | - David Poole
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Athens, Georgia 30332, United States
| | - Piotr Piecuch
- Department of Chemistry and Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Buu Q Pham
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Vladimir Mironov
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Joani Mato
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States
| | - Sam Leonard
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Sarom S Leang
- EP Analytics, Inc., 9909 Mira Mesa Boulevard, Suite 230, San Diego, California 92131, United States
| | - Joe Ivanic
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Jackson Hayes
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Taylor Harville
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Karthik Gururangan
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Emilie Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
| | - Igor S Gerasimov
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Christian Friedl
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Katherine N Ferreras
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - George Elliott
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Dipayan Datta
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Daniel Del Angel Cruz
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Laura Carrington
- EP Analytics, Inc., 9909 Mira Mesa Boulevard, Suite 230, San Diego, California 92131, United States
| | - Colleen Bertoni
- Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Giuseppe M J Barca
- Research School of Computer Science, Australian National University, Canberra, ACT 2601, Australia
| | - Melisa Alkan
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50014, United States
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4
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Kim YL, Evans JW, Gordon MS. Molecular interactions in diffusion-controlled aldol condensation with mesoporous silica nanoparticles. Phys Chem Chem Phys 2022; 24:10475-10487. [PMID: 35441640 DOI: 10.1039/d2cp00952h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The aldol reaction of p-nitrobenzaldehyde in amino-catalyzed mesoporous silica nanoparticles (MSN) has revealed varying catalytic activity with the size of the pores of MSN. The pore size dependence related to the reactivity indicates that the diffusion process is important. A detailed molecular-level analysis for understanding diffusion requires assessment of the noncovalent interactions of the molecular species involved in the aldol reaction with each other, with the solvent, and with key functional groups on the pore surface. Such an analysis is presented here based upon the effective fragment potential (EFP). The EFP method can calculate the intermolecular interactions, decomposed into Coulomb, polarization, dispersion, exchange-repulsion, and charge-transfer interactions. In this study, the potential energy surfaces corresponding to each intermolecular interaction are analyzed for homo- and hetero-dimers with various configurations. The monomers that compose dimers are five molecules such as p-nitrobenzaldehyde, acetone, n-hexane, propylamine, and silanol. The results illustrate that the dispersion interaction is crucial in most dimers.
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Affiliation(s)
- Yu Lim Kim
- Ames Laboratory - US Department of Energy, Iowa State University, Ames, Iowa 50011, USA.,Department of Chemistry, Iowa State University, Ames, Iowa 50010, USA
| | - James W Evans
- Ames Laboratory - US Department of Energy, Iowa State University, Ames, Iowa 50011, USA.,Department of Physics, Iowa State University, Ames, Iowa 50011, USA
| | - Mark S Gordon
- Ames Laboratory - US Department of Energy, Iowa State University, Ames, Iowa 50011, USA.,Department of Chemistry, Iowa State University, Ames, Iowa 50010, USA
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5
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Kim YL, Gordon MS, Garcia A, Evans JW. Rotational and translational diffusion of liquid n-hexane: EFP-based molecular dynamics analysis. J Chem Phys 2022; 156:114503. [DOI: 10.1063/5.0079212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular Dynamics (MD) simulations based on the Effective Fragment Potential (EFP) method are utilized to provide a comprehensive assessment of diffusion in liquid n-hexane. We decompose translational diffusion into components along and orthogonal to the long axis of the molecule. Rotational diffusion is decomposed into tumbling and spinning motions about this axis. Our analysis yields four corresponding diffusion coefficients which are related to diagonal entries in the complete 6 × 6 diffusion tensor accounting for the three rotational and three translational degrees of freedom and for the potential coupling between them. However, coupling between different degrees of freedom is expected to be minimal for a natural choice of the molecular body-fixed axis, so then off-diagonal entries in the tensor are negligible. This expectation is supported by a hydrodynamic analysis of the diffusion tensor which treats the liquid surrounding the molecule being tracked as a viscous continuum. Thus, the EFP MD analysis provides a comprehensive characterization of diffusion and also reveals expected shortcomings of the hydrodynamic treatment, particularly for rotational diffusion, when applied to neat liquids.
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Affiliation(s)
- Yu Lim Kim
- Ames Laboratory – U.S. Department of Energy, Iowa State University, Ames, Iowa 50011, USA
- Department of Chemistry, Iowa State University, Ames, Iowa 50010, USA
| | - Mark S. Gordon
- Ames Laboratory – U.S. Department of Energy, Iowa State University, Ames, Iowa 50011, USA
- Department of Chemistry, Iowa State University, Ames, Iowa 50010, USA
| | - Andres Garcia
- Ames Laboratory – U.S. Department of Energy, Iowa State University, Ames, Iowa 50011, USA
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50010, USA
| | - James W. Evans
- Ames Laboratory – U.S. Department of Energy, Iowa State University, Ames, Iowa 50011, USA
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50010, USA
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6
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Kim YL, Han Y, Evans JW, Gordon MS. Effective Fragment Potential-Based Molecular Dynamics Studies of Diffusion in Acetone and Hexane. J Phys Chem A 2021; 125:3398-3405. [PMID: 33861600 DOI: 10.1021/acs.jpca.1c01865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To facilitate more reliable descriptions of transport properties in liquids, molecular dynamics (MD) simulations are performed based on the effective fragment potential (EFP) method derived from first-principles quantum mechanics (in contrast to MD based upon empirically fitted potentials). The EFP method describes molecular interactions in terms of Coulomb, polarization/induction, dispersion, exchange-repulsion, and charge-transfer interactions. The EFP MD simulations described in this paper, performed on hexane and acetone, are able to track the mean-square displacement of molecules for sufficient time to reliably extract translational diffusion coefficients. The results reported here are in reasonable agreement with experiment.
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Affiliation(s)
- Yu Lim Kim
- Ames Laboratory, US Department of Energy, Iowa State University, Ames, Iowa 50011, United States.,Department of Chemistry, Iowa State University, Ames, Iowa 50010, United States
| | - Yong Han
- Ames Laboratory, US Department of Energy, Iowa State University, Ames, Iowa 50011, United States.,Department of Physics & Astronomy, Iowa State University, Ames, Iowa 50010, United States
| | - James W Evans
- Ames Laboratory, US Department of Energy, Iowa State University, Ames, Iowa 50011, United States.,Department of Physics & Astronomy, Iowa State University, Ames, Iowa 50010, United States
| | - Mark S Gordon
- Ames Laboratory, US Department of Energy, Iowa State University, Ames, Iowa 50011, United States.,Department of Chemistry, Iowa State University, Ames, Iowa 50010, United States
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7
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Barca GMJ, Bertoni C, Carrington L, Datta D, De Silva N, Deustua JE, Fedorov DG, Gour JR, Gunina AO, Guidez E, Harville T, Irle S, Ivanic J, Kowalski K, Leang SS, Li H, Li W, Lutz JJ, Magoulas I, Mato J, Mironov V, Nakata H, Pham BQ, Piecuch P, Poole D, Pruitt SR, Rendell AP, Roskop LB, Ruedenberg K, Sattasathuchana T, Schmidt MW, Shen J, Slipchenko L, Sosonkina M, Sundriyal V, Tiwari A, Galvez Vallejo JL, Westheimer B, Włoch M, Xu P, Zahariev F, Gordon MS. Recent developments in the general atomic and molecular electronic structure system. J Chem Phys 2020; 152:154102. [PMID: 32321259 DOI: 10.1063/5.0005188] [Citation(s) in RCA: 518] [Impact Index Per Article: 129.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods such as the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as it is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite such as GAMESS is maintained and developed is considered. Future developments are briefly summarized.
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Affiliation(s)
- Giuseppe M J Barca
- Research School of Computer Science, Australian National University, Canberra, ACT 2601, Australia
| | - Colleen Bertoni
- Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Laura Carrington
- EP Analytics, 12121 Scripps Summit Dr. Ste. 130, San Diego, California 92131, USA
| | - Dipayan Datta
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Nuwan De Silva
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts 01119, USA
| | - J Emiliano Deustua
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Umezono 1-1-1, Tsukuba 305-8568, Japan
| | - Jeffrey R Gour
- Microsoft, 15590 NE 31st St., Redmond, Washington 98052, USA
| | - Anastasia O Gunina
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Emilie Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, USA
| | - Taylor Harville
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Stephan Irle
- Computational Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Joe Ivanic
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Karol Kowalski
- Physical Sciences Division, Battelle, Pacific Northwest National Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, USA
| | - Sarom S Leang
- EP Analytics, 12121 Scripps Summit Dr. Ste. 130, San Diego, California 92131, USA
| | - Hui Li
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, USA
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jesse J Lutz
- Center for Computing Research, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Ilias Magoulas
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Joani Mato
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Vladimir Mironov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow 119991, Russian Federation
| | - Hiroya Nakata
- Kyocera Corporation, Research Institute for Advanced Materials and Devices, 3-5-3 Hikaridai Seika-cho, Souraku-gun, Kyoto 619-0237, Japan
| | - Buu Q Pham
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Piotr Piecuch
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - David Poole
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Spencer R Pruitt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Alistair P Rendell
- Research School of Computer Science, Australian National University, Canberra, ACT 2601, Australia
| | - Luke B Roskop
- Cray Inc., a Hewlett Packard Enterprise Company, 2131 Lindau Ln #1000, Bloomington, Minnesota 55425, USA
| | - Klaus Ruedenberg
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | | | - Michael W Schmidt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Jun Shen
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Lyudmila Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Masha Sosonkina
- Department of Computational Modeling and Simulation Engineering, Old Dominion University, Norfolk, Virginia 23529, USA
| | - Vaibhav Sundriyal
- Department of Computational Modeling and Simulation Engineering, Old Dominion University, Norfolk, Virginia 23529, USA
| | - Ananta Tiwari
- EP Analytics, 12121 Scripps Summit Dr. Ste. 130, San Diego, California 92131, USA
| | - Jorge L Galvez Vallejo
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Bryce Westheimer
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Marta Włoch
- 530 Charlesina Dr., Rochester, Michigan 48306, USA
| | - Peng Xu
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Federico Zahariev
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
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8
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Tran AL, Guidez EB. Quantum Mechanical Modeling of the Interactions between Noble Metal (Ag and Au) Nanoclusters and Water with the Effective Fragment Potential Method. ACS OMEGA 2020; 5:7446-7455. [PMID: 32280887 PMCID: PMC7144145 DOI: 10.1021/acsomega.0c00132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/13/2020] [Indexed: 06/11/2023]
Abstract
Explicit solvent interactions can significantly alter the physical and chemical properties of noble metal (e.g., gold and silver) nanoclusters. In order to compute these solvent interactions at a reasonable computational cost, a quantum mechanical (QM)/molecular mechanics (MM) approach, where the metal nanocluster is treated with full QM and the water molecules are treated with a MM force field, can be used. However, classical MM force fields were typically parameterized using molecules containing main group elements as the reference. The accuracy of noble metal-solvent interactions obtained with these force fields therefore remains unpredictable. The effective fragment potential (EFP) force field, designed to model explicitly solvated systems, represents an attractive method to simulate solvated noble metal nanoclusters because it is derived from first principles and contains few or no fitted parameters, depending on implementation. At the density functional theory-optimized geometries, good correlation is obtained between the nanocluster-water interaction energies computed with EFP and those computed with the reference coupled cluster singles, doubles, and perturbative triples method. It is shown that the EFP method gives qualitatively accurate interaction energies at medium-large intermolecular distances for various molecular configurations. In order to achieve higher quantitative accuracy, the first solvation shell should be treated with full QM, if possible. EFP is therefore a promising method for the QM modeling of explicitly solvated silver and gold nanoclusters.
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Sattasathuchana T, Xu P, Gordon MS. An Accurate Quantum-Based Approach to Explicit Solvent Effects: Interfacing the General Effective Fragment Potential Method with Ab Initio Electronic Structure Theory. J Phys Chem A 2019; 123:8460-8475. [PMID: 31365250 DOI: 10.1021/acs.jpca.9b05801] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
An interface between ab initio quantum mechanics (QM) methods and the general effective fragment potential (EFP2) method, QM-EFP2, is implemented in which the intermolecular interactions between a QM molecule and EFP fragments consist of Coulomb, polarization, exchange repulsion (exrep), and dispersion components. In order to ensure accuracy in the QM-EFP2 exrep interaction energy, the EFP2-EFP2 spherical Gaussian overlap (SGO) approximation is abandoned and replaced with the exact electron repulsion integrals (ERI) that are evaluated with a direct method to reduce disk usage. A Gaussian damping function for the QM-EFP2 Coulomb component damps both the EFP nuclear and electronic charges. A new overlap damping function has been implemented for the QM-EFP2 dispersion component. The current QM-EFP2 implementation has been benchmarked with the S22 and S66 data sets and demonstrates excellent agreement with symmetry-adapted perturbation theory (SAPT) for component energies and with coupled cluster theory [CCSD(T)] for the total interaction energies. Water clusters of various sizes (up to 256 water molecules) have been tested; it is shown that the QM-EFP2 method has an accuracy that is comparable to that of EFP2-EFP2. It has been shown previously that the accuracy of EFP2-EFP2 intermolecular interactions is comparable to that of second-order perturbation theory (MP2) or better. The implementation of the distributed data interface (DDI) parallelization scheme significantly improves the efficiency of QM-EFP2 calculations. The time to form the QM-EFP2 Fock operator per SCF iteration for water clusters scales linearly with the number EFP basis functions.
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Affiliation(s)
- Tosaporn Sattasathuchana
- Department of Chemistry , Iowa State University and Ames Laboratory Ames , Iowa 50011 , United States
| | - Peng Xu
- Department of Chemistry , Iowa State University and Ames Laboratory Ames , Iowa 50011 , United States
| | - Mark S Gordon
- Department of Chemistry , Iowa State University and Ames Laboratory Ames , Iowa 50011 , United States
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10
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Conrad JA, Kim S, Gordon MS. Ionic liquids from a fragmented perspective. Phys Chem Chem Phys 2019; 21:16878-16888. [PMID: 31359024 DOI: 10.1039/c9cp02836f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The efficacy of using fragmentation methods, such as the effective fragment potential, the fragment molecular orbital and the effective fragment molecular orbital methods is discussed. The advantages and current limitations of these methods are considered, potential improvements are suggested, and a prognosis for the future is provided.
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Affiliation(s)
- Justin A Conrad
- Department of Chemistry, Iowa State University, Ames, IA 50014, USA.
| | - Shinae Kim
- Department of Chemistry, Iowa State University, Ames, IA 50014, USA.
| | - Mark S Gordon
- Department of Chemistry, Iowa State University, Ames, IA 50014, USA.
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11
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Rackers JA, Liu C, Ren P, Ponder JW. A physically grounded damped dispersion model with particle mesh Ewald summation. J Chem Phys 2018; 149:084115. [PMID: 30193468 DOI: 10.1063/1.5030434] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Accurate modeling of dispersion is critical to the goal of predictive biomolecular simulations. To achieve this accuracy, a model must be able to correctly capture both the short-range and asymptotic behavior of dispersion interactions. We present here a damped dispersion model based on the overlap of charge densities that correctly captures both regimes. The overlap damped dispersion model represents a classical physical interpretation of dispersion: the interaction between the instantaneous induced dipoles of two distinct charge distributions. This model is shown to be an excellent fit with symmetry adapted perturbation theory dispersion energy calculations, yielding an RMS error on the S101x7 database of 0.5 kcal/mol. Moreover, the damping function used in this model is wholly derived and parameterized from the electrostatic dipole-dipole interaction, making it not only physically grounded but transferable as well.
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Affiliation(s)
- Joshua A Rackers
- Program in Computational and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jay W Ponder
- Program in Computational and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
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12
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Schoeberle L, Guidez EB, Gordon MS. Benchmarking of the R–7 Anisotropic Dispersion Energy Term on the S22 Dimer Test Set. J Phys Chem A 2018; 122:6100-6108. [DOI: 10.1021/acs.jpca.8b04451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luke Schoeberle
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Emilie B. Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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13
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Kim S, Kaliszewski CM, Guidez EB, Gordon MS. Benchmarking the Effective Fragment Potential Dispersion Correction on the S22 Test Set. J Phys Chem A 2018; 122:4076-4084. [PMID: 29601202 DOI: 10.1021/acs.jpca.7b11628] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The usual modeling of dispersion interactions in density functional theory (DFT) is often limited by the use of empirically fitted parameters. In this study, the accuracies of the popular empirical dispersion corrections and the first-principles derived effective fragment potential (EFP) dispersion correction are compared by computing the DFT-D and HF-D equilibria interaction energies and intermolecular distances of the S22 test set dimers. Functionals based on the local density approximation (LDA) and generalized gradient approximation (GGA), as well as hybrid functionals, are compared for the DFT-D calculations using coupled cluster CCSD(T) at the complete basis set (CBS) limit as the reference method. In general, the HF-D(EFP) method provides accurate equilibrium dimerization energies and intermolecular distances for hydrogen-bonded systems compared to the CCSD(T)/CBS reference data without using any empirical parameters. For dispersion-dominant and mixed systems, the structures and interaction energies obtained with the B3LYP-D(EFP) method are similar to or better than those obtained with the other DFT-D and HF-D methods. Overall, the first-principles derived -D(EFP) correction presents a robust alternative to the empirical -D corrections when used with the B3LYP functional for dispersion-dominant and mixed systems or with Hartree-Fock for hydrogen-bonded systems.
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Affiliation(s)
| | | | - Emilie B Guidez
- Department of Chemistry , University of Colorado Denver , Denver , Colorado 80217 , United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory USDOE , Iowa State University , Ames , Iowa 50011 , United States
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14
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Xu P, Guidez EB, Bertoni C, Gordon MS. Perspective:Ab initioforce field methods derived from quantum mechanics. J Chem Phys 2018. [DOI: 10.1063/1.5009551] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Peng Xu
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Emilie B. Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, USA
| | - Colleen Bertoni
- Argonne Leadership Computing Facility, Argonne, Illinois 60439, USA
| | - Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
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15
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Affiliation(s)
- Emilie B. Guidez
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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16
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Schröder H, Hühnert J, Schwabe T. Evaluation of DFT-D3 dispersion corrections for various structural benchmark sets. J Chem Phys 2017; 146:044115. [DOI: 10.1063/1.4974840] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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17
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Bertoni C, Gordon MS. Analytic Gradients for the Effective Fragment Molecular Orbital Method. J Chem Theory Comput 2016; 12:4743-4767. [DOI: 10.1021/acs.jctc.6b00337] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Colleen Bertoni
- Department of Chemistry, Iowa State University, Ames, Iowa 50014, United States
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50014, United States
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18
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Grimme S, Hansen A, Brandenburg JG, Bannwarth C. Dispersion-Corrected Mean-Field Electronic Structure Methods. Chem Rev 2016; 116:5105-54. [DOI: 10.1021/acs.chemrev.5b00533] [Citation(s) in RCA: 799] [Impact Index Per Article: 99.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
| | | | - Christoph Bannwarth
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
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