1
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Ballesteros F, Lao KU. Analysis of two overlapping fragmentation approaches in density matrix construction: GMBE-DM vs. ADMA. Phys Chem Chem Phys 2024; 26:4386-4394. [PMID: 38236152 DOI: 10.1039/d3cp05759c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
In this study, we conduct a comparative analysis of two density matrix construction methods: the generalized many-body expansion for building density matrices (GMBE-DM) based on the set-theoretical principle of inclusion/exclusion and the adjustable density matrix assembler (ADMA) based on the Mulliken-Mezey ansatz. We apply these methods to various noncovalent clusters, including water clusters, ion-water clusters, and ion-pair clusters, using both small 6-31G(d) and large def2-TZVPPD basis sets. Our findings reveal that the GMBE-DM method, particularly when combined with the purification scheme and truncation at the one-body level [GMBE(1)-DM-P], exhibits superior performance across all test systems and basis sets. In contrast, all ADMA set of methods show reasonable results only with small and compact basis sets. For example, GMBE(1)-DM-P outperforms the best ADMA method by at least 4 and 16 times with small and large basis sets, respectively, in the case of (H2O)N=6-55. This highlights the significance of the basis set choice for ADMA, which is even more critical than the fragmentation scheme, such as the size of subsystems, while GMBE-DM consistently produces accurate results irrespective of the chosen basis set. Consequently, the efficient and robust GMBE(1)-DM-P approach is recommended as a fragmentation method for generating accurate absolute and relative energies across different binding patterns and basis sets for noncovalent clusters.
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Affiliation(s)
| | - Ka Un Lao
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA.
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2
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Broderick DR, Herbert JM. Scalable generalized screening for high-order terms in the many-body expansion: Algorithm, open-source implementation, and demonstration. J Chem Phys 2023; 159:174801. [PMID: 37921253 DOI: 10.1063/5.0174293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023] Open
Abstract
The many-body expansion lies at the heart of numerous fragment-based methods that are intended to sidestep the nonlinear scaling of ab initio quantum chemistry, making electronic structure calculations feasible in large systems. In principle, inclusion of higher-order n-body terms ought to improve the accuracy in a controllable way, but unfavorable combinatorics often defeats this in practice and applications with n ≥ 4 are rare. Here, we outline an algorithm to overcome this combinatorial bottleneck, based on a bottom-up approach to energy-based screening. This is implemented within a new open-source software application ("Fragme∩t"), which is integrated with a lightweight semi-empirical method that is used to cull subsystems, attenuating the combinatorial growth of higher-order terms in the graph that is used to manage the calculations. This facilitates applications of unprecedented size, and we report four-body calculations in (H2O)64 clusters that afford relative energies within 0.1 kcal/mol/monomer of the supersystem result using less than 10% of the unique subsystems. We also report n-body calculations in (H2O)20 clusters up to n = 8, at which point the expansion terminates naturally due to screening. These are the largest n-body calculations reported to date using ab initio electronic structure theory, and they confirm that high-order n-body terms are mostly artifacts of basis-set superposition error.
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Affiliation(s)
- Dustin R Broderick
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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3
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Sahu N, Khire SS, Gadre SR. Combining fragmentation method and high-performance computing: Geometry optimization and vibrational spectra of proteins. J Chem Phys 2023; 159:044309. [PMID: 37522406 DOI: 10.1063/5.0149572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023] Open
Abstract
Exploring the structures and spectral features of proteins with advanced quantum chemical methods is an uphill task. In this work, a fragment-based molecular tailoring approach (MTA) is appraised for the CAM-B3LYP/aug-cc-pVDZ-level geometry optimization and vibrational infrared (IR) spectra calculation of ten real proteins containing up to 407 atoms and 6617 basis functions. The use of MTA and the inherently parallel nature of the fragment calculations enables a rapid and accurate calculation of the IR spectrum. The applicability of MTA to optimize the protein geometry and evaluate its IR spectrum employing a polarizable continuum model with water as a solvent is also showcased. The typical errors in the total energy and IR frequencies computed by MTA vis-à-vis their full calculation (FC) counterparts for the studied protein are 5-10 millihartrees and 5 cm-1, respectively. Moreover, due to the independent execution of the fragments, large-scale parallelization can also be achieved. With increasing size and level of theory, MTA shows an appreciable advantage in computer time as well as memory and disk space requirement over the corresponding FCs. The present study suggests that the geometry optimization and IR computations on the biomolecules containing ∼1000 atoms and/or ∼15 000 basis functions using MTA and HPC facility can be clearly envisioned in the near future.
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Affiliation(s)
- Nityananda Sahu
- Theoretische Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Subodh S Khire
- RIKEN Center for Computational Science, Kobe 650-0047, Japan
| | - Shridhar R Gadre
- Departments of Scientific Computing, Modelling & Simulation and Chemistry, Savitribai Phule Pune University, Pune 411007, India
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4
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Malloum A, Conradie J. Hydrogen bond networks of dimethylsulfoxide (DMSO) pentamer. J Mol Graph Model 2023; 118:108363. [PMID: 36308947 DOI: 10.1016/j.jmgm.2022.108363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/05/2022] [Accepted: 10/11/2022] [Indexed: 11/28/2022]
Abstract
Understanding of clusters of dimethylsulfoxide (DMSO) is important in several applications in Chemistry. Despite its importance, very few studies of DMSO clusters, (DMSO)n, have been reported in comparison to systems such as water clusters or methanol clusters. In order to provide further understanding of DMSO clusters, we investigated the structures and non-covalent interactions of the (DMSO)n, n=5. Therefore, the potential energy surface (PES) of the DMSO pentamer has been examined using classical molecular dynamics. The structures generated using classical molecular dynamics are further optimized at the PW6B95D3/aug-cc-pVDZ level of theory. To comprehend the non-covalent bondings in the DMSO pentamer, we carried out a quantum theory of atoms in molecule (QTAIM) analysis. In addition, the effects of temperature on the structural stability is investigated between 20 and 500K. It comes out that seven different kind of non-covalent bondings can be found in DMSO pentamers.
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Affiliation(s)
- Alhadji Malloum
- Department of Chemistry, University of the Free State, PO BOX 339, Bloemfontein 9300, South Africa; Department of Physics, Faculty of Science, University of Maroua, PO BOX 46, Maroua, Cameroon.
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, PO BOX 339, Bloemfontein 9300, South Africa; Department of Chemistry, UiT - The Arctic University of Norway, N-9037 Tromsø, Norway
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5
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Hellmers J, König C. A unified and flexible formulation of molecular fragmentation schemes. J Chem Phys 2021; 155:164105. [PMID: 34717347 DOI: 10.1063/5.0059598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We present a flexible formulation for energy-based molecular fragmentation schemes. This framework does not only incorporate the majority of existing fragmentation expansions but also allows for flexible formulation of novel schemes. We further illustrate its application in multi-level approaches and for electronic interaction energies. For the examples of small water clusters, a small protein, and protein-protein interaction energies, we show how this flexible setup can be exploited to generate a well-suited multi-level fragmentation expansion for the given case. With such a setup, we reproduce the electronic protein-protein interaction energy of ten different structures of a neurotensin and an extracellular loop of its receptor with a mean absolute deviation to the respective super-system calculations below 1 kJ/mol.
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Affiliation(s)
- Janine Hellmers
- Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, Hannover, Germany
| | - Carolin König
- Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, Hannover, Germany
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Chedid J, Jocelyn N, Eshuis H. Energies, structures, and harmonic frequencies of small water clusters from the direct random phase approximation. J Chem Phys 2021; 155:084303. [PMID: 34470345 DOI: 10.1063/5.0059343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The binding energies, structures, and vibrational frequencies of water clusters up to 20 molecules are computed at the direct random phase approximation (RPA) level of theory and compared to theoretical benchmarks. Binding energies of the WATER27 set, which includes neutral and positively and negatively charged clusters, are predicted to be too low in the complete basis set limit by an average of 7 kcal/mol (9%) and are worse than the results from the best density functional theory methods or from the Møller-Plesset theory. The RPA shows significant basis set size dependence for binding energies. The order of the relative energies of the water hexamer and dodecamer isomers is predicted correctly by the RPA. The mean absolute deviation for angles and distances for neutral clusters up to the water hexamer are 0.2° and 0.6 pm, respectively, using quintuple-ζ basis sets. The relative energetic order of the hexamer isomers is preserved upon optimization. Vibrational frequencies for these systems are underestimated by several tens of wavenumbers for large basis sets, and deviations increase with the basis set size. Overall, the direct RPA method yields accurate structural parameters but systematically underestimates binding energies and shows strong basis set size dependence.
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Affiliation(s)
- Julianna Chedid
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, New Jersey 07043, USA
| | - Nedjie Jocelyn
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, New Jersey 07043, USA
| | - Henk Eshuis
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, New Jersey 07043, USA
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7
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Malloum A, Conradie J. Hydrogen bond networks of ammonia clusters: What we know and what we don’t know. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116199] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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8
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Tripathy V, Saha A, Raghavachari K. Electrostatically embedded molecules-in-molecules approach and its application to molecular clusters. J Comput Chem 2021; 42:719-734. [PMID: 33586802 DOI: 10.1002/jcc.26492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/25/2020] [Accepted: 01/16/2021] [Indexed: 11/06/2022]
Abstract
We report the application of our fragment-based quantum chemistry model MIM (Molecules-In-Molecules) with electrostatic embedding. The method is termed "EE-MIM (Electrostatically Embedded Molecules-In-Molecules)" and accounts for the missing electrostatic interactions in the subsystems resulting from fragmentation. Point charges placed at the atomic positions are used to represent the interaction of each subsystem with the rest of the molecule with minimal increase in the computational cost. We have carefully calibrated this model on a range of different sizes of clusters containing up to 57 water molecules. The fragmentation methods have been applied with the goal of reproducing the unfragmented total energy at the MP2/6-311G(d,p) level. Comparative analysis has been carried out between MIM and EE-MIM to gauge the impact of electrostatic embedding. Performance of several different parameters such as the type of charge and levels of fragmentation are analyzed for the prediction of absolute energies. The use of background charges in subsystem calculations improves the performance of both one- and two-layer MIM while it is noticeably important in the case of one-layer MIM. Embedded charges for two-layer MIM are obtained from a full system calculation at the low-level. For one-layer MIM, in the absence of a full system calculation, two different types of embedded charges, namely, Geometry dependent (GD) and geometry independent (GI) charges, are used. A self-consistent procedure is employed to obtain GD charges. We have further tested our method on challenging charged systems with stronger intermolecular interactions, namely, protonated ammonia clusters (containing up to 30 ammonia molecules). The observations are similar to water clusters with improved performance using embedded charges. Overall, the performance of NPA charges as embedded charges is found to be the best.
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Affiliation(s)
- Vikrant Tripathy
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Arjun Saha
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
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9
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Szabó PB, Csóka J, Kállay M, Nagy PR. Linear-Scaling Open-Shell MP2 Approach: Algorithm, Benchmarks, and Large-Scale Applications. J Chem Theory Comput 2021; 17:2886-2905. [PMID: 33819030 PMCID: PMC8154337 DOI: 10.1021/acs.jctc.1c00093] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
A linear-scaling
local second-order Møller–Plesset
(MP2) method is presented for high-spin open-shell molecules based
on restricted open-shell (RO) reference functions. The open-shell
local MP2 (LMP2) approach inherits the iteration- and redundancy-free
formulation and the completely integral-direct, OpenMP-parallel, and
memory and disk use economic algorithms of our closed-shell LMP2 implementation.
By utilizing restricted local molecular orbitals for the demanding
integral transformation step and by introducing a novel long-range
spin-polarization approximation, the computational cost of RO-LMP2
approaches that of closed-shell LMP2. Extensive benchmarks were performed
for reactions of radicals, ionization potentials, as well as spin-state
splittings of carbenes and transition-metal complexes. Compared to
the conventional MP2 reference for systems of up to 175 atoms, local
errors of at most 0.1 kcal/mol were found, which are well below the
intrinsic accuracy of MP2. RO-LMP2 computations are presented for
challenging protein models of up to 601 atoms and 11 000 basis
functions, which involve either spin states of a complexed iron ion
or a highly delocalized singly occupied orbital. The corresponding
runtimes of 9–15 h obtained with a single, many-core CPU demonstrate
that MP2, as well as spin-scaled MP2 and double-hybrid density functional
methods, become widely accessible for open-shell systems of unprecedented
size and complexity.
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Affiliation(s)
- P Bernát Szabó
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - József Csóka
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Mihály Kállay
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Péter R Nagy
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
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10
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Malloum A, Conradie J. Structures of water clusters in the solvent phase and relative stability compared to gas phase. Polyhedron 2021. [DOI: 10.1016/j.poly.2020.114856] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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12
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Cheng Z, Zhao D, Ma J, Li W, Li S. An On-the-Fly Approach to Construct Generalized Energy-Based Fragmentation Machine Learning Force Fields of Complex Systems. J Phys Chem A 2020; 124:5007-5014. [DOI: 10.1021/acs.jpca.0c04526] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Zheng Cheng
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Dongbo Zhao
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Jing Ma
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Wei Li
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Shuhua Li
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
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13
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Zhou J, Zhu L, Chen J, Wang W, Zhang R, Li Y, Zhang Q, Wang W. Degradation mechanism for Zearalenone ring-cleavage by Zearalenone hydrolase RmZHD: A QM/MM study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 709:135897. [PMID: 31887512 DOI: 10.1016/j.scitotenv.2019.135897] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/01/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
The danger of zearalenone (ZEN) as an endocrine disruptor to humans and the environment has aroused increasing attention. In this study, we implemented the quantum mechanics/molecular mechanics (QM/MM) method to investigate the degradation mechanism of ZEN hydrolase (RmZHD) toward ZEN at the atomic level. The degradation process involves two concerted reaction pathways, where the active site contains a Ser-His-Glu triplet as a proton donor. With the Boltzmann-weighted average potential barriers of 18.1 and 21.5 kcal/mol, the process undergoes proton transfer and nucleophilic-substituted ring opening to form a hydroxyl product. Non-covalent interaction analyses elucidated hydrogen bonding between key amino acids with ZEN. The electrostatic influence analysis of 16 amino acids proposes residues Asp34 and His128 as the possible mutation target for future mutation design of enzyme RmZHD. An in-depth investigation of the protein environment of RmZHD can improve the bioremediation efficiency of endocrine disrupting chemicals.
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Affiliation(s)
- Jie Zhou
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Ledong Zhu
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Jinfeng Chen
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Wei Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Ruiming Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China.
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
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14
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Malloum A, Fifen JJ, Conradie J. Large-Sized Ammonia Clusters and Solvation Energies of the Proton in Ammonia. J Comput Chem 2020; 41:21-30. [PMID: 31568565 DOI: 10.1002/jcc.26071] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/19/2019] [Accepted: 08/28/2019] [Indexed: 01/10/2023]
Abstract
The absolute solvation energies (free energies and enthalpies) of the proton in ammonia are used to compute the pKa of species embedded in ammonia. They are also used to compute the solvation energies of other ions in ammonia. Despite their importance, it is not possible to determine experimentally the solvation energies of the proton in a given solvent. We propose in this work a direct approach to compute the solvation energies of the proton in ammonia from large-sized neutral and protonated ammonia clusters. To undertake this investigation, we performed a geometry optimization of neutral and protonated ammonia 30-mer, 40-mer, and 50 mer to locate stable structures. These structures have been fully optimized at both APFD/6-31++g(d,p) and M06-2X/6-31++g(d,p) levels of theory. An infrared spectroscopic study of these structures has been provided to assess the reliability of our investigation. Using these structures, we have computed the absolute solvation free energy and the absolute solvation enthalpy of the proton in ammonia. It comes out that the absolute solvation free energy of the proton in ammonia is calculated to be -1192 kJ mol-1 , whereas the absolute solvation enthalpy is evaluated to be -1214 kJ mol-1 . © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Alhadji Malloum
- Department of Chemistry, University of the Free State, Bloemfontein, 9300, South Africa
| | - Jean J Fifen
- Department of Physics, Faculty of Science, The University of Ngaoundere, 454, Ngaoundere, Cameroon
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, Bloemfontein, 9300, South Africa
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15
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Gyevi-Nagy L, Kállay M, Nagy PR. Integral-Direct and Parallel Implementation of the CCSD(T) Method: Algorithmic Developments and Large-Scale Applications. J Chem Theory Comput 2019; 16:366-384. [DOI: 10.1021/acs.jctc.9b00957] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- László Gyevi-Nagy
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
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16
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Veccham SP, Lee J, Head-Gordon M. Making many-body interactions nearly pairwise additive: The polarized many-body expansion approach. J Chem Phys 2019; 151:194101. [DOI: 10.1063/1.5125802] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Srimukh Prasad Veccham
- Department of Chemistry, University of California, Berkeley, California 94720 USA, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Joonho Lee
- Department of Chemistry, University of California, Berkeley, California 94720 USA, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720 USA, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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17
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Abstract
Since the introduction of the fragment molecular orbital method 20 years ago, fragment-based approaches have occupied a small but growing niche in quantum chemistry. These methods decompose a large molecular system into subsystems small enough to be amenable to electronic structure calculations, following which the subsystem information is reassembled in order to approximate an otherwise intractable supersystem calculation. Fragmentation sidesteps the steep rise (with respect to system size) in the cost of ab initio calculations, replacing it with a distributed cost across numerous computer processors. Such methods are attractive, in part, because they are easily parallelizable and therefore readily amenable to exascale computing. As such, there has been hope that distributed computing might offer the proverbial "free lunch" in quantum chemistry, with the entrée being high-level calculations on very large systems. While fragment-based quantum chemistry can count many success stories, there also exists a seedy underbelly of rarely acknowledged problems. As these methods begin to mature, it is time to have a serious conversation about what they can and cannot be expected to accomplish in the near future. Both successes and challenges are highlighted in this Perspective.
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Affiliation(s)
- John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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18
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Nagy PR, Kállay M. Approaching the Basis Set Limit of CCSD(T) Energies for Large Molecules with Local Natural Orbital Coupled-Cluster Methods. J Chem Theory Comput 2019; 15:5275-5298. [DOI: 10.1021/acs.jctc.9b00511] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Péter R. Nagy
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Mihály Kállay
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
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19
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Liu J, Rana B, Liu KY, Herbert JM. Variational Formulation of the Generalized Many-Body Expansion with Self-Consistent Charge Embedding: Simple and Correct Analytic Energy Gradient for Fragment-Based ab Initio Molecular Dynamics. J Phys Chem Lett 2019; 10:3877-3886. [PMID: 31251619 DOI: 10.1021/acs.jpclett.9b01214] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The many-body expansion (MBE) and its extension to overlapping fragments, the generalized (G)MBE, constitute the theoretical basis for most fragment-based approaches for large-scale quantum chemistry. We reformulate the GMBE for use with embedding charges determined self-consistently from the fragment wave functions, in a manner that preserves the variational nature of the underlying self-consistent field method. As a result, the analytic gradient retains the simple "sum of fragment gradients" form that is often assumed in practice, sometimes incorrectly. This obviates (without approximation) the need to solve coupled-perturbed equations, and we demonstrate stable, fragment-based ab initio molecular dynamics simulations using this technique. Energy conservation fails when charge-response contributions to the Fock matrix are neglected, even while geometry optimizations and vibrational frequency calculations may yet be accurate. Stable simulations can be recovered by means of straightforward modifications introduced here, providing a general paradigm for fragment-based ab initio molecular dynamics.
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Affiliation(s)
- Jie Liu
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Bhaskar Rana
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Kuan-Yu Liu
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - John M Herbert
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
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20
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Bakó I, Mayer I, Hamza A, Pusztai L. Two- and three-body, and relaxation energy terms in water clusters: Application of the hierarchical BSSE corrected decomposition scheme. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.04.088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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21
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Khire SS, Gadre SR. Pragmatic Many-Body Approach for Economic MP2 Energy Estimation of Molecular Clusters. J Phys Chem A 2019; 123:5005-5011. [PMID: 31117601 DOI: 10.1021/acs.jpca.9b03481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We propose a procedure, within the many-body analysis (MBA) framework, for an economic yet accurate estimation of the correlated method-based energies of large molecular clusters employing Dunning's augmented basis sets. The basis of the procedure is to segregate the Hartree-Fock ( EHF) and correlation energy ( EC) estimations. EHF is found to differ by tens of millihartrees (mH) from its full-calculation (FC) counterpart on truncating the MBA expansion at the two-body (MBA-2) level. On the contrary, EC is estimated with smaller error on modest hardware with limited computation time at the (MBA-2) level. In view of this, we adopt a pragmatic method wherein the EHF (accurate to five decimal places) is taken from the FC, whereas EC is estimated at the MBA-2 level. This method is applied to a variety of medium to large molecular clusters at the MP2 level. Preliminary results at the CCSD(T) level for (H2O)16 and (H2O)17 are also reported with tremendous savings in wall-clock time and resources. The typical errors in MP2 and CCSD(T) energies per monomer are up to 0.1 and 0.2 mH, respectively. Thus the present method, balancing accuracy and computational economy, opens a way for estimating energies of large molecular clusters using correlated theories with large basis sets.
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Affiliation(s)
- Subodh S Khire
- Interdisciplinary School of Scientific Computing , Savitribai Phule Pune University , Pune 411007 , India
| | - Shridhar R Gadre
- Interdisciplinary School of Scientific Computing , Savitribai Phule Pune University , Pune 411007 , India
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22
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Malloum A, Fifen JJ, Dhaouadi Z, Nana Engo SG, Conradie J. Structures, relative stability and binding energies of neutral water clusters, (H2O)2–30. NEW J CHEM 2019. [DOI: 10.1039/c9nj01659g] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have revised the structures of neutral water clusters, (H2O)n=2–30, with the affordable M06-2X functional, presenting up to 25 isomers for each cluster size.
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Affiliation(s)
- Alhadji Malloum
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jean Jules Fifen
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Zoubeida Dhaouadi
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications
- Faculté des Sciences de Tunis
- Université de Tunis El Manar
- Tunis
- Tunisia
| | - Serge Guy Nana Engo
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
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23
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Khire SS, Bartolotti LJ, Gadre SR. Harmonizing accuracy and efficiency: A pragmatic approach to fragmentation of large molecules. J Chem Phys 2018; 149:064112. [PMID: 30111143 DOI: 10.1063/1.5036595] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Fragmentation methods offer an attractive alternative for ab initio treatment of large molecules and molecular clusters. However, balancing the accuracy and efficiency of these methods is a tight-rope-act. With this in view, we present an algorithm for automatic molecular fragmentation within Molecular Tailoring Approach (MTA) achieving this delicate balance. The automated code is tested out on a variety of molecules and clusters at the Hartree-Fock (HF)- and Møller-Plesset second order perturbation theory as well as density functional theory employing augmented Dunning basis sets. The results show remarkable accuracy and efficiency vis-à-vis the respective full calculations. Thus the present work forms an important step toward the development of an MTA-based black box code for implementation of HF as well as correlated quantum chemical calculations on large molecular systems.
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Affiliation(s)
- Subodh S Khire
- Interdisciplinary School of Scientific Computing, Savitribai Phule Pune University, Pune 411007, India
| | - Libero J Bartolotti
- Department of Physical and Computational Chemistry, East Carolina University, Greenville, North Carolina 27858, USA
| | - Shridhar R Gadre
- Interdisciplinary School of Scientific Computing, Savitribai Phule Pune University, Pune 411007, India
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24
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Nagy PR, Samu G, Kállay M. Optimization of the Linear-Scaling Local Natural Orbital CCSD(T) Method: Improved Algorithm and Benchmark Applications. J Chem Theory Comput 2018; 14:4193-4215. [DOI: 10.1021/acs.jctc.8b00442] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Péter R. Nagy
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Gyula Samu
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Mihály Kállay
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
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25
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Hofer TS, Hünenberger PH. Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration. J Chem Phys 2018; 148:222814. [DOI: 10.1063/1.5000799] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Centre for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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26
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Wu X, Clavaguera C, Lagardère L, Piquemal JP, de la Lande A. AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms. J Chem Theory Comput 2018; 14:2705-2720. [PMID: 29630819 DOI: 10.1021/acs.jctc.7b01128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We report the first parameters of the heme redox cofactors for the polarizable AMOEBA force field in both the ferric and ferrous forms. We consider two types of complexes, one with two histidine side chains as axial ligands and one with a histidine and a methionine side chain as ligands. We have derived permanent multipoles from second-order Møller-Plesset perturbation theory (MP2). The sets of parameters have been validated in a first step by comparison of AMOEBA interaction energies of heme and a collection of biologically relevant molecules with MP2 and Density Functional Theory (DFT) calculations. In a second validation step, we consider interaction energies with large aggregates comprising around 80 H2O molecules. These calculations are repeated for 30 structures extracted from semiempirical PM7 DM simulations. Very encouraging agreement is found between DFT and the AMOEBA force field, which results from an accurate treatment of electrostatic interactions. We finally report long (10 ns) MD simulations of cytochromes in two redox states with AMOEBA testing both the 2003 and 2014 AMOEBA water models. These simulations have been carried out with the TINKER-HP (High Performance) program. In conclusion, owing to their ubiquity in biology, we think the present work opens a wide array of applications of the polarizable AMOEBA force field on hemeproteins.
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Affiliation(s)
- Xiaojing Wu
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
| | - Carine Clavaguera
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
| | - Louis Lagardère
- Sorbonne Université, CNRS , Institut Parisien de Chimie Physique et Théorique (IP2CT) , 4 Place Jussieu , F-75005 , Paris , France.,Sorbonne Université , Institut des Sciences du Calcul et des Données (ISCD) , 4 place Jussieu , F-75005 , Paris , France
| | - Jean-Philip Piquemal
- Sorbonne Université, CNRS , Laboratoire de Chimie Théorique (LCT) , 4 Place Jussieu , F-75005 , Paris , France.,Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States.,Institut Universitaire de France , 75005 , Paris , France
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
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27
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Li Y, Yuan D, Wang Q, Li W, Li S. Accurate prediction of the structure and vibrational spectra of ionic liquid clusters with the generalized energy-based fragmentation approach: critical role of ion-pair-based fragmentation. Phys Chem Chem Phys 2018; 20:13547-13557. [DOI: 10.1039/c8cp00513c] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The GEBF method with the ion-pair-based fragmentation has been developed to facilitate ab initio calculations of general ionic liquid clusters.
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Affiliation(s)
- Yunzhi 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
| | - Dandan Yuan
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Qingchun Wang
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - 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
| | - Shuhua 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
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28
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Yuan D, Li Y, Li W, Li S. Structures and properties of large supramolecular coordination complexes predicted with the generalized energy-based fragmentation method. Phys Chem Chem Phys 2018; 20:28894-28902. [DOI: 10.1039/c8cp05548c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The generalized energy-based fragmentation (GEBF) method has been extended to facilitate ab initio calculations of large supramolecular coordination complexes.
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Affiliation(s)
- Dandan Yuan
- 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
| | - Yunzhi 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
| | - 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
| | - Shuhua 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
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29
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Liu KY, Herbert JM. Understanding the many-body expansion for large systems. III. Critical role of four-body terms, counterpoise corrections, and cutoffs. J Chem Phys 2017; 147:161729. [DOI: 10.1063/1.4986110] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Kuan-Yu Liu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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