1
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Li J, Yang W. Chemical Potentials and the One-Electron Hamiltonian of the Second-Order Perturbation Theory from the Functional Derivative Approach. J Phys Chem A 2024; 128:4876-4885. [PMID: 38842399 DOI: 10.1021/acs.jpca.4c01574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
We develop a functional derivative approach to calculate the chemical potentials of second-order perturbation theory (MP2). In the functional derivative approach, the correlation part of the MP2 chemical potential, which is the derivative of the MP2 correlation energy with respect to the occupation number of frontier orbitals, is obtained from the chain rule via the noninteracting Green's function. First, the MP2 correlation energy is expressed in terms of the noninteracting Green's function, and its functional derivative to the noninteracting Green's function is the second-order self-energy. Then, the derivative of the noninteracting Green's function to the occupation number is obtained by including the orbital relaxation effect. We show that the MP2 chemical potentials obtained from the functional derivative approach agree with that obtained from the finite difference approach. The one-electron Hamiltonian, defined as the derivative of the MP2 energy with respect to the one particle density matrix, is also derived using the functional derivative approach, which can be used in the self-consistent calculations of MP2 and double-hybrid density functionals. The developed functional derivative approach is promising for calculating the chemical potentials and the one-electron Hamiltonian of approximate functionals and many-body perturbation approaches dependent explicitly on the noninteracting Green's function.
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Affiliation(s)
- Jiachen Li
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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2
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Kuan KY, Yeh SH, Yang W, Hsu CP. Excited-State Charge Transfer Coupling from Quasiparticle Energy Density Functional Theory. J Phys Chem Lett 2024; 15:6126-6136. [PMID: 38830203 PMCID: PMC11181311 DOI: 10.1021/acs.jpclett.4c00850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 06/05/2024]
Abstract
The recently developed Quasiparticle Energy (QE) scheme, based on a DFT calculation with one more (or less) electron, offers a good description of excitation energies, even with charge transfer characters. In this work, QE is further extended to calculate electron transfer (ET) couplings involving two excited states. We tested it with a donor-acceptor complex, consisting of a furan and a 1,1-dicyanoethylene (DCNE), in which two low lying charge transfer and local excitation states are involved. With generalized Mülliken-Hush and fragment charge-difference schemes, couplings from the QE approach generally agree well with those obtained from TDDFT, except that QE couplings exhibit better exponential distance dependence. Couplings from half-energy gaps with an external field are also calculated and reported. Our results show that the QE scheme is robust in calculating ET couplings with greatly reduced computational time.
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Affiliation(s)
- Kai-Yuan Kuan
- Institute
of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang
District, Taipei 11529, Taiwan
| | - Shu-Hao Yeh
- Institute
of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang
District, Taipei 11529, Taiwan
- Department
of Chemistry, National Taiwan University, 1 Roosevelt Rd, Section 4, Da’an
District, Taipei City 10617, Taiwan
| | - Weitao Yang
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Chao-Ping Hsu
- Institute
of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang
District, Taipei 11529, Taiwan
- Division
of Physics, National Center for Theoretical
Sciences, 1 Roosevelt
Road, Section 4, Taipei City 10617, Taiwan
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3
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Ju CW, Shen Y, French EJ, Yi J, Bi H, Tian A, Lin Z. Accurate Electronic and Optical Properties of Organic Doublet Radicals Using Machine Learned Range-Separated Functionals. J Phys Chem A 2024. [PMID: 38382058 DOI: 10.1021/acs.jpca.3c07437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Luminescent organic semiconducting doublet-spin radicals are unique and emergent optical materials because their fluorescent quantum yields (Φfl) are not compromised by the spin-flipping intersystem crossing (ISC) into a dark high-spin state. The multiconfigurational nature of these radicals challenges their electronic structure calculations in the framework of single-reference density functional theory (DFT) and introduces room for method improvement. In the present study, we extended our earlier development of ML-ωPBE [J. Phys. Chem. Lett., 2021, 12, 9516-9524], a range-separated hybrid (RSH) exchange-correlation (XC) functional constructed using the stacked ensemble machine learning (SEML) algorithm, from closed-shell organic semiconducting molecules to doublet-spin organic semiconducting radicals. We assessed its performance for a new test set of 64 doublet-spin radicals from five categories while placing all previously compiled 3926 closed-shell molecules in the new training set. Interestingly, ML-ωPBE agrees with the nonempirical OT-ωPBE functional regarding the prediction of the molecule-dependent range-separation parameter (ω), with a small mean absolute error (MAE) of 0.0197 a0-1, but saves the computational cost by 2.46 orders of magnitude. This result demonstrates an outstanding domain adaptation capacity of ML-ωPBE for diverse organic semiconducting species. To further assess the predictive power of ML-ωPBE in experimental observables, we also applied it to evaluate absorption and fluorescence energies (Eabs and Efl) using linear-response time-dependent DFT (TDDFT), and we compared its behavior with nine popular XC functionals. For most radicals, ML-ωPBE reproduces experimental measurements of Eabs and Efl with small MAEs of 0.299 and 0.254 eV, only marginally different from those of OT-ωPBE. Our work illustrates a successful extension of the SEML framework from closed-shell molecules to doublet-spin radicals and will open the venue for calculating optical properties for organic semiconductors using single-reference TDDFT.
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Affiliation(s)
- Cheng-Wei Ju
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, United States
| | - Yili Shen
- Manning College of Information and Computer Sciences, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Ethan J French
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Jun Yi
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Hongshan Bi
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Aaron Tian
- Manning College of Information and Computer Sciences, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Zhou Lin
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
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4
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Hu F, Wang Y, Zeng J, Deng X, Xia F, Xu X. Unveiling the State Transition Mechanisms of Ras Proteins through Enhanced Sampling and QM/MM Simulations. J Phys Chem B 2024; 128:1418-1427. [PMID: 38323538 DOI: 10.1021/acs.jpcb.3c07666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
In cells, wild-type RasGTP complexes exist in two distinct states: active State 2 and inactive State 1. These complexes regulate their functions by transitioning between the two states. However, the mechanisms underlying this state transition have not been clearly elucidated. To address this, we conducted a detailed simulation study to characterize the energetics of the stable states involved in the state transitions of the HRasGTP complex, specifically from State 2 to State 1. This was achieved by employing multiscale quantum mechanics/molecular mechanics and enhanced sampling molecular dynamics methods. Based on the simulation results, we constructed the two-dimensional free energy landscapes that provide crucial information about the conformational changes of the HRasGTP complex from State 2 to State 1. Furthermore, we also explored the conformational changes from the intermediate state to the product state during guanosine triphosphate hydrolysis. This study on the conformational changes involved in the HRas state transitions serves as a valuable reference for understanding the corresponding events of both KRas and NRas as well.
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Affiliation(s)
- Fangchen Hu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Yiqiu Wang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Juan Zeng
- School of Biomedical Engineering, Guangdong Medical University, Dongguan 523808, China
| | - Xianming Deng
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Fei Xia
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai 200433, China
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5
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Santra G, Cho M, Martin JML. Correction to "Exploring Avenues beyond Revised DSD Functionals: I. Range Separation, with xDSD as a Special Case". J Phys Chem A 2024; 128:974-975. [PMID: 38291588 PMCID: PMC11027754 DOI: 10.1021/acs.jpca.4c00309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Indexed: 02/01/2024]
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6
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Yang S, Zhang IY, Ren X. Developing correlation-consistent numeric atom-centered orbital basis sets for krypton: Applications in RPA-based correlated calculations. J Chem Phys 2024; 160:024112. [PMID: 38193553 DOI: 10.1063/5.0174952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/04/2023] [Indexed: 01/10/2024] Open
Abstract
Localized atomic orbitals are the preferred basis set choice for large-scale explicit correlated calculations, and high-quality hierarchical correlation-consistent basis sets are a prerequisite for correlated methods to deliver numerically reliable results. At present, numeric atom-centered orbital (NAO) basis sets with valence correlation consistency (VCC), designated as NAO-VCC-nZ, are only available for light elements from hydrogen (H) to argon (Ar) [Zhang et al., New J. Phys. 15, 123033 (2013)]. In this work, we extend this series by developing NAO-VCC-nZ basis sets for krypton (Kr), a prototypical element in the fourth row of the periodic table. We demonstrate that NAO-VCC-nZ basis sets facilitate the convergence of electronic total-energy calculations using the Random Phase Approximation (RPA), which can be used together with a two-point extrapolation scheme to approach the complete basis set limit. Notably, the Basis Set Superposition Error (BSSE) associated with the newly generated NAO basis sets is minimal, making them suitable for applications where BSSE correction is either cumbersome or impractical to do. After confirming the reliability of NAO basis sets for Kr, we proceed to calculate the Helmholtz free energy for Kr crystal at the theoretical level of RPA plus renormalized single excitation correction. From this, we derive the pressure-volume (P-V) diagram, which shows excellent agreement with the latest experimental data. Our work demonstrates the capability of correlation-consistent NAO basis sets for heavy elements, paving the way toward numerically reliable correlated calculations for bulk materials.
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Affiliation(s)
- Sixian Yang
- Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, China
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Igor Ying Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai, Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xinguo Ren
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
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7
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Aloui M, Er-rajy M, Imtara H, Goudzal A, Zarougui S, El fadili M, Arthur DE, Mothana RA, Noman OM, Tarayrah M, Menana E. QSAR modelling, molecular docking, molecular dynamic and ADMET prediction of pyrrolopyrimidine derivatives as novel Bruton's tyrosine kinase (BTK) inhibitors. Saudi Pharm J 2024; 32:101911. [PMID: 38226346 PMCID: PMC10788635 DOI: 10.1016/j.jsps.2023.101911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/07/2023] [Indexed: 01/17/2024] Open
Abstract
In recent years, there has been a focus on developing and discovering novel Bruton's tyrosine kinase (BTK) inhibitors, as they offer an effective treatment strategy for B-cell malignancies. BTK plays a crucial role in B cell receptor (BCR)-mediated activation and proliferation by regulating downstream factors such as the NF-κB and MAP kinase pathways. To address this challenge and propose potential therapeutic options for B-cell lymphomas, researchers conducted 2D-QSAR and ADMET studies on pyrrolopyrimidine derivatives that act as inhibitors of the BCR site in cytochrome b. These studies aim to improve and identify new compounds that could serve as more potent potential BTK inhibitors, which would lead to the identification of new drug candidates in this field. In our study, we used 2D-QSAR (multiple linear regression, multiple nonlinear regression, and artificial neural networks), molecular docking, molecular dynamics, and ADMET properties to investigate the potential of 35 pyrrolopyrimidine derivatives as BTK inhibitors. A molecular docking study and molecular dynamics simulations of molecule 13 over 10 ns revealed that it establishes multiple hydrogen bonds with several residues and exhibits frequent stability throughout the simulation period. Based on the results obtained by molecular modeling, we proposed six new compounds (Pred1, Pred2, Pred3, Pred4, Pred5, and Pred6) with highly significant predicted activity by MLR models. A study based on the in silico evaluation of the predicted ADMET properties of the new candidate molecules is strongly recommended to classify these molecules as promising candidates for new anticancer agents specifically designed to target Bruton's tyrosine kinase (BTK) inhibition.
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Affiliation(s)
- Mourad Aloui
- LIMAS Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohammed Er-rajy
- LIMAS Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Hamada Imtara
- Faculty of Sciences, Arab American University Palestine, Jenin 44862, Palestine
| | - Amina Goudzal
- Engineering Laboratory of Organometallic, Molecular Materials and Environment, Sidi Mohamed Ben Abdellah University, Faculty of Sciences, Fez, Morocco
| | - Sara Zarougui
- LIMAS Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohamed El fadili
- LIMAS Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - David E. Arthur
- Department of Pure and Applied Chemistry, University of Maiduguri, Nigeria
| | - Ramzi A. Mothana
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Omar M. Noman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mahmoud Tarayrah
- Groupe Hospitalier Cochin-Port Royal, Faculty of Medicine, Institut Cochin, Paris University, CNRS, IN-SERM, 75000, Paris, France
| | - Elhalaoui Menana
- LIMAS Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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8
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Fu B, Zhang DH. Accurate fundamental invariant-neural network representation of ab initio potential energy surfaces. Natl Sci Rev 2023; 10:nwad321. [PMID: 38274241 PMCID: PMC10808953 DOI: 10.1093/nsr/nwad321] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 01/27/2024] Open
Abstract
Highly accurate potential energy surfaces are critically important for chemical reaction dynamics. The large number of degrees of freedom and the intricate symmetry adaption pose a big challenge to accurately representing potential energy surfaces (PESs) for polyatomic reactions. Recently, our group has made substantial progress in this direction by developing the fundamental invariant-neural network (FI-NN) approach. Here, we review these advances, demonstrating that the FI-NN approach can represent highly accurate, global, full-dimensional PESs for reactive systems with even more than 10 atoms. These multi-channel reactions typically involve many intermediates, transition states, and products. The complexity and ruggedness of this potential energy landscape present even greater challenges for full-dimensional PES representation. These PESs exhibit a high level of complexity, molecular size, and accuracy of fit. Dynamics simulations based on these PESs have unveiled intriguing and novel reaction mechanisms, providing deep insights into the intricate dynamics involved in combustion, atmospheric, and organic chemistry.
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Affiliation(s)
- Bina Fu
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Hefei National Laboratory, Hefei 230088, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Hefei National Laboratory, Hefei 230088, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Komarov K, Park W, Lee S, Huix-Rotllant M, Choi CH. Doubly Tuned Exchange-Correlation Functionals for Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory. J Chem Theory Comput 2023; 19:7671-7684. [PMID: 37844129 DOI: 10.1021/acs.jctc.3c00884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
It is demonstrated that significant accuracy improvements in MRSF-TDDFT can be achieved by introducing two different exchange-correlation (XC) functionals for the reference Kohn-Sham DFT and the response part of the calculations, respectively. Accordingly, two new XC functionals of doubly tuned Coulomb attenuated method-vertical excitation energy (DTCAM-VEE) and DTCAM-AEE were developed on the basis of the "adaptive exact exchange (AEE)" concept in the framework of the Coulomb-attenuating XC functionals. The values by DTCAM-VEE are in excellent agreement with those of Thiel's set [mean absolute errors (MAEs) and the interquartile range (IQR) values of 0.218 and 0.327 eV, respectively]. On the other hand, DTCAM-AEE faithfully reproduced the qualitative aspects of conical intersections (CIs) of trans-butadiene and thymine and the nonadiabatic molecular dynamics (NAMD) simulations on thymine. The latter functional also remarkably exhibited the exact 1/R asymptotic behavior of the charge-transfer state of an ethylene-tetrafluoroethylene dimer and the accurate potential energy surfaces (PESs) along the two torsional angles of retinal protonated Schiff base model with six double bonds (rPSB6). Overall, DTCAM-AEE generally performs well, as its MAE (0.237) and IQR (0.41 eV) are much improved as compared to BH&HLYP. The current idea can also be applied to other XC functionals as well as other variants of linear response theories, opening a new way of developing XC functionals.
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Affiliation(s)
- Konstantin Komarov
- Center for Quantum Dynamics, Pohang University of Science and Technology, Pohang 37673, South Korea
| | - Woojin Park
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Seunghoon Lee
- Department of Chemistry, Seoul National University, Seoul, 151-747, South Korea
| | | | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
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10
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Daas KJ, Kooi DP, Peters NC, Fabiano E, Della Sala F, Gori-Giorgi P, Vuckovic S. Regularized and Opposite Spin-Scaled Functionals from Møller-Plesset Adiabatic Connection─Higher Accuracy at Lower Cost. J Phys Chem Lett 2023; 14:8448-8459. [PMID: 37721318 DOI: 10.1021/acs.jpclett.3c01832] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Noncovalent interactions (NCIs) play a crucial role in biology, chemistry, material science, and everything in between. To improve pure quantum-chemical simulations of NCIs, we propose a methodology for constructing approximate correlation energies by combining an interpolation along the Møller-Plesset adiabatic connection (MP AC) with a regularization and spin-scaling strategy applied to MP2 correlation energies. This combination yields cosκos-SPL2, which exhibits superior accuracy for NCIs compared to any of the individual strategies. With the N4 formal scaling, cosκos-SPL2 is competitive or often outperforms more expensive dispersion-corrected double hybrids for NCIs. The accuracy of cosκos-SPL2 particularly shines for anionic halogen bonded complexes, where it surpasses standard dispersion-corrected DFT by a factor of 3 to 5.
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Affiliation(s)
- Kimberly J Daas
- Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Derk P Kooi
- Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
- Microsoft Research AI4Science, Evert van de Beekstraat 354, 1118CZ Schiphol, The Netherlands
| | - Nina C Peters
- Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Eduardo Fabiano
- Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia, 73010 Arnesano, Italy
| | - Fabio Della Sala
- Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia, 73010 Arnesano, Italy
| | - Paola Gori-Giorgi
- Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
- Microsoft Research AI4Science, Evert van de Beekstraat 354, 1118CZ Schiphol, The Netherlands
| | - Stefan Vuckovic
- Department of Chemistry, Faculty of Science and Medicine, Université de Fribourg/Universität Freiburg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
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11
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Lehtola S, Marques MAL. Reproducibility of density functional approximations: How new functionals should be reported. J Chem Phys 2023; 159:114116. [PMID: 37725491 DOI: 10.1063/5.0167763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 08/28/2023] [Indexed: 09/21/2023] Open
Abstract
Density functional theory is the workhorse of chemistry and materials science, and novel density functional approximations are published every year. To become available in program packages, the novel density functional approximations (DFAs) need to be (re)implemented. However, according to our experience as developers of Libxc [Lehtola et al., SoftwareX 7, 1 (2018)], a constant problem in this task is verification due to the lack of reliable reference data. As we discuss in this work, this lack has led to several non-equivalent implementations of functionals such as Becke-Perdew 1986, Perdew-Wang 1991, Perdew-Burke-Ernzerhof, and Becke's three-parameter hybrid functional with Lee-Yang-Parr correlation across various program packages, yielding different total energies. Through careful verification, we have also found many issues with incorrect functional forms in recent DFAs. The goal of this work is to ensure the reproducibility of DFAs. DFAs must be verifiable in order to prevent the reappearance of the above-mentioned errors and incompatibilities. A common framework for verification and testing is, therefore, needed. We suggest several ways in which reference energies can be produced with free and open source software, either with non-self-consistent calculations with tabulated atomic densities or via self-consistent calculations with various program packages. The employed numerical parameters-especially the quadrature grid-need to be converged to guarantee a ≲0.1 μEh precision in the total energy, which is nowadays routinely achievable in fully numerical calculations. Moreover, as such sub-μEh level agreement can only be achieved when fully equivalent implementations of the DFA are used, the source code of the reference implementation should also be made available in any publication describing a new DFA.
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Affiliation(s)
- Susi Lehtola
- Molecular Sciences Software Institute, Blacksburg, Virginia 24061, USA
- Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Miguel A L Marques
- Research Center Future Energy Materials and Systems of the University Alliance Ruhr, Faculty of Mechanical Engineering, Ruhr University Bochum, Universitätsstraße 150, D-44801 Bochum, Germany
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12
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Becke AD, Santra G, Martin JML. A double-hybrid density functional based on good local physics with outstanding performance on the GMTKN55 database. J Chem Phys 2023; 158:2882268. [PMID: 37094004 DOI: 10.1063/5.0141238] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/20/2023] [Indexed: 04/26/2023] Open
Abstract
In two recent papers [A. D. Becke, J. Chem. Phys. 156, 214101 (2022) and A. D. Becke, J. Chem. Phys. 157, 234102 (2022)], we compared two Kohn-Sham density functionals based on physical modeling and theory with the best density-functional power-series fits in the literature. The best error statistics reported to date for a hybrid functional on the general main-group thermochemistry, kinetics, and noncovalent interactions (GMTKN55) chemical database of Goerigk et al. [Phys. Chem. Chem. Phys. 19, 32184 (2017)] were obtained. In the present work, additional second-order perturbation-theory terms are considered. The result is a 12-parameter double-hybrid density functional with the lowest GMTKN55 WTMAD2 "weighted total mean absolute deviation" error (1.76 kcal/mol) yet seen for any hybrid or double-hybrid density-functional approximation. We call it "DH23."
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Affiliation(s)
- Axel D Becke
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada
| | - Golokesh Santra
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Jan M L Martin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Rehovot, Israel
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13
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Morgante P, Peverati R. Comparison of the Performance of Density Functional Methods for the Description of Spin States and Binding Energies of Porphyrins. Molecules 2023; 28:molecules28083487. [PMID: 37110720 PMCID: PMC10146789 DOI: 10.3390/molecules28083487] [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: 03/28/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
This work analyzes the performance of 250 electronic structure theory methods (including 240 density functional approximations) for the description of spin states and the binding properties of iron, manganese, and cobalt porphyrins. The assessment employs the Por21 database of high-level computational data (CASPT2 reference energies taken from the literature). Results show that current approximations fail to achieve the "chemical accuracy" target of 1.0 kcal/mol by a long margin. The best-performing methods achieve a mean unsigned error (MUE) <15.0 kcal/mol, but the errors are at least twice as large for most methods. Semilocal functionals and global hybrid functionals with a low percentage of exact exchange are found to be the least problematic for spin states and binding energies, in agreement with the general knowledge in transition metal computational chemistry. Approximations with high percentages of exact exchange (including range-separated and double-hybrid functionals) can lead to catastrophic failures. More modern approximations usually perform better than older functionals. An accurate statistical analysis of the results also casts doubts on some of the reference energies calculated using multireference methods. Suggestions and general guidelines for users are provided in the conclusions. These results hopefully stimulate advances for both the wave function and the density functional side of electronic structure calculations.
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Affiliation(s)
- Pierpaolo Morgante
- Department of Chemistry and Chemical Engineering, Florida Institute of Technology, 150 W. University Blvd., Melbourne, FL 32901, USA
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Roberto Peverati
- Department of Chemistry and Chemical Engineering, Florida Institute of Technology, 150 W. University Blvd., Melbourne, FL 32901, USA
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14
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Chen B, Xu X. Discriminating and understanding molecular crystal polymorphism. J Comput Chem 2023; 44:969-979. [PMID: 36585855 DOI: 10.1002/jcc.27057] [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: 09/04/2022] [Revised: 11/01/2022] [Accepted: 11/30/2022] [Indexed: 01/01/2023]
Abstract
Polymorph discrimination for a molecular crystal has long been a challenging task, which, nonetheless, is a major concern in the pharmaceutical industry. In this work, we have investigated polymorph discrimination on three different molecular crystals, tetrolic acid, oxalic acid, and oxalyl dihydrazide, covering both packing polymorphism and conformational polymorphism. To gain more understanding, we have performed energy decomposition analysis based on many-body expansion, and have compared the results from the XO-PBC method, that is, the eXtended ONIOM method (XO) with the periodic boundary condition (PBC), with those from some commonly used dispersion corrected density functional theory (DFT-D) methods. It is shown here that, with the XYG3 doubly hybrid functional chosen as the target high level to capture the intra- and short-range intermolecular interactions, and the periodic PBE as the basic low level to take long range interactions into account, the XO-PBC(XYG3:PBE) method not only obtains the correct experimental stability orderings, but also predicts reasonable polymorph energy ranges for all three cases. Our results have demonstrated the usefulness of the present theoretical methods, in particular XO-PBC, while highlighted the importance of a better treatment of different kinds of interactions to be beneficial to polymorph control.
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Affiliation(s)
- Bozhu Chen
- Department of Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Fudan University, Shanghai, China
| | - Xin Xu
- Department of Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Fudan University, Shanghai, China.,Hefei National Laboratory, Hefei, China
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15
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Upadhyaya HP. Theoretical study on the gas phase hydroxyl radical reaction with tetrahydrothiophene, tetrahydrofuran, thiophene and furan. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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16
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Chen Z, Liu Z, Xu X. Accurate descriptions of molecule-surface interactions in electrocatalytic CO 2 reduction on the copper surfaces. Nat Commun 2023; 14:936. [PMID: 36807556 PMCID: PMC9941474 DOI: 10.1038/s41467-023-36695-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Copper-based catalysts play a pivotal role in many industrial processes and hold a great promise for electrocatalytic CO2 reduction reaction into valuable chemicals and fuels. Towards the rational design of catalysts, the growing demand on theoretical study is seriously at odds with the low accuracy of the most widely used functionals of generalized gradient approximation. Here, we present results using a hybrid scheme that combines the doubly hybrid XYG3 functional and the periodic generalized gradient approximation, whose accuracy is validated against an experimental set on copper surfaces. A near chemical accuracy is established for this set, which, in turn, leads to a substantial improvement for the calculated equilibrium and onset potentials as against the experimental values for CO2 reduction to CO on Cu(111) and Cu(100) electrodes. We anticipate that the easy use of the hybrid scheme will boost the predictive power for accurate descriptions of molecule-surface interactions in heterogeneous catalysis.
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Affiliation(s)
- Zheng Chen
- grid.8547.e0000 0001 0125 2443Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, 200433 Shanghai, People’s Republic of China
| | - Zhangyun Liu
- grid.8547.e0000 0001 0125 2443Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, 200433 Shanghai, People’s Republic of China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, 200433, Shanghai, People's Republic of China. .,Hefei National Laboratory, 230088, Hefei, P. R. China.
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17
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Tokmachev AM. Statistical Equivalence of Quantum Chemical Methods for Energy Distribution in Water Clusters. Chemphyschem 2023; 24:e202300019. [PMID: 36787108 DOI: 10.1002/cphc.202300019] [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: 01/09/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/15/2023]
Abstract
Methods of quantum chemistry are instrumental in understanding molecular structures and properties. However, the results demonstrate significant variability, which is difficult to predict and rationalize. The fundamental question is whether some molecular systems exhibit properties invariant with respect to the computational method. The idea explored here is that collective properties of statistical ensembles should be more robust than characteristics of individual molecules and their arbitrary sets. This effect is demonstrated for the complete set of hydrogen-bond topologies of the dodecahedral water cluster (H2 O)20 . Non-Gaussian energy distributions produced by various methods have the same functional form despite strong differences in mean values and standard deviations. The conclusion is tested on methods of different complexity and origin employing a number of criteria. A linear mapping between the energies produced by different methods is discussed. The significance of the results is in establishing a collective equivalence property of quantum chemical methods.
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Affiliation(s)
- Andrey M Tokmachev
- National Research Center "Kurchatov Institute", Kurchatov Sq. 1, 123182, Moscow, Russia
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18
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Zhou J, Jia S, Xue X, Hao X, Zeng Q, Wang X, Ren X. Structural and dynamical studies of CH- πbonded CH 4-C 6H 6dimer by ultrafast intermolecular Coulombic decay. NANOTECHNOLOGY 2023; 34:165102. [PMID: 36645904 DOI: 10.1088/1361-6528/acb358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
The inner-valence ionization and fragmentation dynamics of CH4-C6H6dimer induced by 200 eV electron impact is studied utilizing a multi-particle coincidence momentum spectroscopy. The three-dimensional momentum vectors and kinetic energy release (KER) of the CH4++C6H6+ion pairs are obtained by coincident momentum measurement. Our analysis on the absolute cross sections indicates that the intermediate dication CH4+-C6H6+is preferentially produced by the removal of an inner-valence electron from CH4or C6H6and subsequent relaxation of ultrafast intermolecular Coulombic decay followed by two-body Coulomb explosion. Combining withab initiomolecular dynamics (AIMD) simulations, the real-time fragmentation dynamics including translational, vibrational and rotational motions are presented as a function of propagation time. The revealed fragmentation dynamics are expected to have a potential implication for crystal structure imaging with various radiation sources.
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Affiliation(s)
- Jiaqi Zhou
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Shaokui Jia
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Xiaorui Xue
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Xintai Hao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Qingrui Zeng
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Xing Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Xueguang Ren
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
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19
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Sandoval-Salinas ME, Brémond E, Pérez-Jiménez AJ, Adamo C, Sancho-García JC. Excitation energies of polycylic aromatic hydrocarbons by double-hybrid functionals: Assessing the PBE0-DH and PBE-QIDH models and their range-separated versions. J Chem Phys 2023; 158:044105. [PMID: 36725511 DOI: 10.1063/5.0134946] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A family of non-empirical double-hybrid (DH) density functionals, such as Perdew-Burke-Ernzerhof (PBE)0-DH, PBE-QIDH, and their range-separated exchange (RSX) versions RSX-0DH and RSX-QIDH, all using Perdew-Burke-Ernzerhof(PBE) exchange and correlationfunctionals, is applied here to calculate the excitation energies for increasingly longer linear and cyclic acenes as part of their intense benchmarking for excited states of all types. The energies for the two lowest-lying singlet 1La and 1Lb states of linear oligoacenes as well as the triplet 3La and 3Lb states, are calculated and compared with experimental results. These functionals clearly outperform the results obtained from hybrid functionals and favorably compare with other double-hybrid expressions also tested here, such as B2-PLYP, B2GP-PLYP, ωB2-PLYP, and ωB2GP-PLYP. The study is complemented by the computation of adiabatic S0-T1 singlet-triplet energy difference for linear acenes as well as the extension of the study to strained cyclic oligomers, showing how the family of non-empirical expressions robustly leads to competitive results.
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Affiliation(s)
- M E Sandoval-Salinas
- Department of Physical Chemistry, University of Alicante, E-03080 Alicante, Spain
| | - E Brémond
- ITODYS, CNRS, Université Paris Cité, F-75006 Paris, France
| | - A J Pérez-Jiménez
- Department of Physical Chemistry, University of Alicante, E-03080 Alicante, Spain
| | - C Adamo
- Chimie ParisTech, CNRS, Institute of Chemistry for Life and Health Sciences (i-CLeHS), UMR8060, PSL Research University, F-75005 Paris, France
| | - J C Sancho-García
- Department of Physical Chemistry, University of Alicante, E-03080 Alicante, Spain
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20
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Inversion Theory Leveling as a New Methodological Approach to Antioxidant Thermodynamics: A Case Study on Phenol. Antioxidants (Basel) 2023; 12:antiox12020282. [PMID: 36829841 PMCID: PMC9952401 DOI: 10.3390/antiox12020282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/31/2023] Open
Abstract
Antioxidants are various types of compounds that represent a link between biology and chemistry. With the development of theoretical and computational methods, antioxidants are now being studied theoretically. Here, a novel method is presented that aims to reduce the estimated wall times for DFT calculations that result in the same or higher degree of accuracy in the second derivatives over energy than is the case with the regular computational route (i.e., optimizing the reaction system at a lower model and then recalculating the energies at a higher level of theory) by applying the inversion of theory level to the universal chemical scavenger model, i.e., phenol. The resulting accuracy and wall time obtained with such a methodological setup strongly suggest that this methodology could be generally applied to antioxidant thermodynamics for some costly DFT methods with relative absolute deviation.
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21
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Curtis K, Adeyiga O, Suleiman O, Odoh SO. Building on the strengths of a double-hybrid density functional for excitation energies and inverted singlet-triplet energy gaps. J Chem Phys 2023; 158:024116. [PMID: 36641391 DOI: 10.1063/5.0133727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
It is demonstrated that a double hybrid density functional approximation, ωB88PTPSS, that incorporates equipartition of density functional theory and the non-local correlation, however with a meta-generalized gradient approximation correlation functional, as well as with the range-separated exchange of ωB2PLYP, provides accurate excitation energies for conventional systems, as well as correct prescription of negative singlet-triplet gaps for non-conventional systems with inverted gaps, without any necessity for parametric scaling of the same-spin and opposite-spin non-local correlation energies. Examined over "safe" excitations of the QUESTDB set, ωB88PTPSS performs quite well for open-shell systems, correctly and fairly accurately [relative to equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) reference] predicts negative gaps for 50 systems with inverted singlet-triplet gaps, and is one of the leading performers for intramolecular charge-transfer excitations and achieves near-second-order approximate coupled cluster (CC2) and second-order algebraic diagrammatic construction quality for the Q1 and Q2 subsets. Subsequently, we tested ωB88PTPSS on two sets of real-life examples from recent computational chemistry literature-the low energy bands of chlorophyll a (Chl a) and a set of thermally activated delayed fluorescence (TADF) systems. For Chl a, ωB88PTPSS qualitatively and quantitatively achieves DLPNO-STEOM-CCSD-level performance and provides excellent agreement with experiment. For TADF systems, ωB88PTPSS agrees quite well with spin-component-scaled CC2 (SCS-CC2) excitation energies, as well as experimental values, for the gaps between the S1 and T1 excited states.
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Affiliation(s)
- Kevin Curtis
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Olajumoke Adeyiga
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Olabisi Suleiman
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Samuel O Odoh
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
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22
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Krep L, Schmalz F, Solbach F, Komissarov L, Nevolianis T, Kopp WA, Verstraelen T, Leonhard K. A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part II: A ChemTraYzer Study of Chlorinated Dibenzofuran Formation and Decomposition Processes. Chemphyschem 2022; 24:e202200783. [PMID: 36511423 DOI: 10.1002/cphc.202200783] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/14/2022]
Abstract
In our two-paper series, we first present the development of ReaxFF CHOCl parameters using the recently published ParAMS parametrization tool. In this second part, we update the reactive Molecular Dynamics - Quantum Mechanics coupling scheme ChemTraYzer and combine it with our new ReaxFF parameters from Part I to study formation and decomposition processes of chlorinated dibenzofurans. We introduce a self-learning method for recovering failed transition-state searches that improves the overall ChemTraYzer transition-state search success rate by 10 percentage points to a total of 48 %. With ChemTraYzer, we automatically find and quantify more than 500 reactions using transition state theory and DFT. Among the discovered chlorinated dibenzofuran reactions are numerous reactions that are new to the literature. In three case studies, we discuss the set of reactions that are most relevant to the dibenzofuran literature: (i) bimolecular reactions of the chlorinated-dibenzofuran precursors phenoxy radical and 1,3,5-trichlorobenzene, (ii) dibenzofuran chlorination and pyrolysis, and (iii) oxidation of chlorinated dibenzofurans.
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Affiliation(s)
- Lukas Krep
- Institute of Technical Thermodynamics, RWTH Aachen University, North Rhine-Westphalia, 52062, Aachen, Germany
| | - Felix Schmalz
- Institute of Technical Thermodynamics, RWTH Aachen University, North Rhine-Westphalia, 52062, Aachen, Germany
| | - Florian Solbach
- Institute of Technical Thermodynamics, RWTH Aachen University, North Rhine-Westphalia, 52062, Aachen, Germany
| | - Leonid Komissarov
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark-Zwijnaarde 46, B-9052, Ghent, Belgium
| | - Thomas Nevolianis
- Institute of Technical Thermodynamics, RWTH Aachen University, North Rhine-Westphalia, 52062, Aachen, Germany
| | - Wassja A Kopp
- Institute of Technical Thermodynamics, RWTH Aachen University, North Rhine-Westphalia, 52062, Aachen, Germany
| | - Toon Verstraelen
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark-Zwijnaarde 46, B-9052, Ghent, Belgium
| | - Kai Leonhard
- Institute of Technical Thermodynamics, RWTH Aachen University, North Rhine-Westphalia, 52062, Aachen, Germany
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23
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Yang Z, Wan Z, Liu L, Fu J, Fan Q, Xie F, Zhang Y, Ma J. Achieving vibrational energies of diatomic systems with high quality by machine learning improved DFT method. RSC Adv 2022; 12:35950-35958. [PMID: 36545113 PMCID: PMC9753899 DOI: 10.1039/d2ra07613f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
When using ab initio methods to obtain high-quality quantum behavior of molecules, it often involves a lot of trial-and-error work in algorithm design and parameter selection, which requires enormous time and computational resource costs. In the study of vibrational energies of diatomic molecules, we found that starting from a low-precision DFT model and then correcting the errors using the high-dimensional function modeling capabilities of machine learning, one can considerably reduce the computational burden and improve the prediction accuracy. Data-driven machine learning is able to capture subtle physical information that is missing from DFT approaches. The results of 12C16O, 24MgO and Na35Cl show that, compared with CCSD(T)/cc-pV5Z calculation, this work improves the prediction accuracy by more than one order of magnitude, and reduces the computation cost by more than one order of magnitude.
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Affiliation(s)
- Zhangzhang Yang
- School of science, Key Laboratory of High Performance Scientific Computation, Xihua UniversityChengdu610039China
| | - Zhitao Wan
- School of science, Key Laboratory of High Performance Scientific Computation, Xihua UniversityChengdu610039China
| | - Li Liu
- School of science, Key Laboratory of High Performance Scientific Computation, Xihua UniversityChengdu610039China
| | - Jia Fu
- School of science, Key Laboratory of High Performance Scientific Computation, Xihua UniversityChengdu610039China
| | - Qunchao Fan
- School of science, Key Laboratory of High Performance Scientific Computation, Xihua UniversityChengdu610039China
| | - Feng Xie
- Institute of Nuclear and New Energy Technology, Collaborative Innovation Center of Advanced Nuclear Energy Technology, Key Laboratory of Advanced Reactor Engineering and Safety of Ministry of Education, Tsinghua UniversityBeijing100084China
| | - Yi Zhang
- College of Advanced Interdisciplinary Studies, National University of Defense TechnologyChangsha410073China
| | - Jie Ma
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Laser Spectroscopy Laboratory, College of Physics and Electronics Engineering, Shanxi UniversityTaiyuan030006China
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24
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Teale AM, Helgaker T, Savin A, Adamo C, Aradi B, Arbuznikov AV, Ayers PW, Baerends EJ, Barone V, Calaminici P, Cancès E, Carter EA, Chattaraj PK, Chermette H, Ciofini I, Crawford TD, De Proft F, Dobson JF, Draxl C, Frauenheim T, Fromager E, Fuentealba P, Gagliardi L, Galli G, Gao J, Geerlings P, Gidopoulos N, Gill PMW, Gori-Giorgi P, Görling A, Gould T, Grimme S, Gritsenko O, Jensen HJA, Johnson ER, Jones RO, Kaupp M, Köster AM, Kronik L, Krylov AI, Kvaal S, Laestadius A, Levy M, Lewin M, Liu S, Loos PF, Maitra NT, Neese F, Perdew JP, Pernal K, Pernot P, Piecuch P, Rebolini E, Reining L, Romaniello P, Ruzsinszky A, Salahub DR, Scheffler M, Schwerdtfeger P, Staroverov VN, Sun J, Tellgren E, Tozer DJ, Trickey SB, Ullrich CA, Vela A, Vignale G, Wesolowski TA, Xu X, Yang W. DFT exchange: sharing perspectives on the workhorse of quantum chemistry and materials science. Phys Chem Chem Phys 2022; 24:28700-28781. [PMID: 36269074 PMCID: PMC9728646 DOI: 10.1039/d2cp02827a] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/09/2022] [Indexed: 12/13/2022]
Abstract
In this paper, the history, present status, and future of density-functional theory (DFT) is informally reviewed and discussed by 70 workers in the field, including molecular scientists, materials scientists, method developers and practitioners. The format of the paper is that of a roundtable discussion, in which the participants express and exchange views on DFT in the form of 302 individual contributions, formulated as responses to a preset list of 26 questions. Supported by a bibliography of 777 entries, the paper represents a broad snapshot of DFT, anno 2022.
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Affiliation(s)
- Andrew M. Teale
- School of Chemistry, University of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Trygve Helgaker
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway.
| | - Andreas Savin
- Laboratoire de Chimie Théorique, CNRS and Sorbonne University, 4 Place Jussieu, CEDEX 05, 75252 Paris, France.
| | - Carlo Adamo
- PSL University, CNRS, ChimieParisTech-PSL, Institute of Chemistry for Health and Life Sciences, i-CLeHS, 11 rue P. et M. Curie, 75005 Paris, France.
| | - Bálint Aradi
- Bremen Center for Computational Materials Science, University of Bremen, P.O. Box 330440, D-28334 Bremen, Germany.
| | - Alexei V. Arbuznikov
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7Straße des 17. Juni 13510623Berlin
| | | | - Evert Jan Baerends
- Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands.
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy.
| | - Patrizia Calaminici
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav), CDMX, 07360, Mexico.
| | - Eric Cancès
- CERMICS, Ecole des Ponts and Inria Paris, 6 Avenue Blaise Pascal, 77455 Marne-la-Vallée, France.
| | - Emily A. Carter
- Department of Mechanical and Aerospace Engineering and the Andlinger Center for Energy and the Environment, Princeton UniversityPrincetonNJ 08544-5263USA
| | | | - Henry Chermette
- Institut Sciences Analytiques, Université Claude Bernard Lyon1, CNRS UMR 5280, 69622 Villeurbanne, France.
| | - Ilaria Ciofini
- PSL University, CNRS, ChimieParisTech-PSL, Institute of Chemistry for Health and Life Sciences, i-CLeHS, 11 rue P. et M. Curie, 75005 Paris, France.
| | - T. Daniel Crawford
- Department of Chemistry, Virginia TechBlacksburgVA 24061USA,Molecular Sciences Software InstituteBlacksburgVA 24060USA
| | - Frank De Proft
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium.
| | | | - Claudia Draxl
- Institut für Physik and IRIS Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany. .,Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
| | - Thomas Frauenheim
- Bremen Center for Computational Materials Science, University of Bremen, P.O. Box 330440, D-28334 Bremen, Germany. .,Beijing Computational Science Research Center (CSRC), 100193 Beijing, China.,Shenzhen JL Computational Science and Applied Research Institute, 518110 Shenzhen, China
| | - Emmanuel Fromager
- Laboratoire de Chimie Quantique, Institut de Chimie, CNRS/Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France.
| | - Patricio Fuentealba
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile.
| | - Laura Gagliardi
- Department of Chemistry, Pritzker School of Molecular Engineering, The James Franck Institute, and Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.
| | - Giulia Galli
- Pritzker School of Molecular Engineering and Department of Chemistry, The University of Chicago, Chicago, IL, USA.
| | - Jiali Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China. .,Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Paul Geerlings
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Nikitas Gidopoulos
- Department of Physics, Durham University, South Road, Durham DH1 3LE, UK.
| | - Peter M. W. Gill
- School of Chemistry, University of SydneyCamperdown NSW 2006Australia
| | - Paola Gori-Giorgi
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands.
| | - Andreas Görling
- Chair of Theoretical Chemistry, University of Erlangen-Nuremberg, Egerlandstrasse 3, 91058 Erlangen, Germany.
| | - Tim Gould
- Qld Micro- and Nanotechnology Centre, Griffith University, Gold Coast, Qld 4222, Australia.
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany.
| | - Oleg Gritsenko
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands.
| | - Hans Jørgen Aagaard Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark.
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie UniversityHalifaxNova ScotiaB3H 4R2Canada
| | - Robert O. Jones
- Peter Grünberg Institut PGI-1, Forschungszentrum Jülich52425 JülichGermany
| | - Martin Kaupp
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Straße des 17. Juni 135, 10623, Berlin.
| | - Andreas M. Köster
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav)CDMX07360Mexico
| | - Leeor Kronik
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovoth, 76100, Israel.
| | - Anna I. Krylov
- Department of Chemistry, University of Southern CaliforniaLos AngelesCalifornia 90089USA
| | - Simen Kvaal
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway.
| | - Andre Laestadius
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway.
| | - Mel Levy
- Department of Chemistry, Tulane University, New Orleans, Louisiana, 70118, USA.
| | - Mathieu Lewin
- CNRS & CEREMADE, Université Paris-Dauphine, PSL Research University, Place de Lattre de Tassigny, 75016 Paris, France.
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, NC 27599-3420, USA. .,Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, France.
| | - Neepa T. Maitra
- Department of Physics, Rutgers University at Newark101 Warren StreetNewarkNJ 07102USA
| | - Frank Neese
- Max Planck Institut für Kohlenforschung, Kaiser Wilhelm Platz 1, D-45470 Mülheim an der Ruhr, Germany.
| | - John P. Perdew
- Departments of Physics and Chemistry, Temple UniversityPhiladelphiaPA 19122USA
| | - Katarzyna Pernal
- Institute of Physics, Lodz University of Technology, ul. Wolczanska 219, 90-924 Lodz, Poland.
| | - Pascal Pernot
- Institut de Chimie Physique, UMR8000, CNRS and Université Paris-Saclay, Bât. 349, Campus d'Orsay, 91405 Orsay, France.
| | - Piotr Piecuch
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA. .,Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA
| | - Elisa Rebolini
- Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France.
| | - Lucia Reining
- Laboratoire des Solides Irradiés, CNRS, CEA/DRF/IRAMIS, École Polytechnique, Institut Polytechnique de Paris, F-91120 Palaiseau, France. .,European Theoretical Spectroscopy Facility
| | - Pina Romaniello
- Laboratoire de Physique Théorique (UMR 5152), Université de Toulouse, CNRS, UPS, France.
| | - Adrienn Ruzsinszky
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA.
| | - Dennis R. Salahub
- Department of Chemistry, Department of Physics and Astronomy, CMS – Centre for Molecular Simulation, IQST – Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary2500 University Drive NWCalgaryAlbertaT2N 1N4Canada
| | - Matthias Scheffler
- The NOMAD Laboratory at the FHI of the Max-Planck-Gesellschaft and IRIS-Adlershof of the Humboldt-Universität zu Berlin, Faradayweg 4-6, D-14195, Germany.
| | - Peter Schwerdtfeger
- Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study, Massey University Auckland, 0632 Auckland, New Zealand.
| | - Viktor N. Staroverov
- Department of Chemistry, The University of Western OntarioLondonOntario N6A 5B7Canada
| | - Jianwei Sun
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA.
| | - Erik Tellgren
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway.
| | - David J. Tozer
- Department of Chemistry, Durham UniversitySouth RoadDurhamDH1 3LEUK
| | - Samuel B. Trickey
- Quantum Theory Project, Deptartment of Physics, University of FloridaGainesvilleFL 32611USA
| | - Carsten A. Ullrich
- Department of Physics and Astronomy, University of MissouriColumbiaMO 65211USA
| | - Alberto Vela
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav), CDMX, 07360, Mexico.
| | - Giovanni Vignale
- Department of Physics, University of Missouri, Columbia, MO 65203, USA.
| | - Tomasz A. Wesolowski
- Department of Physical Chemistry, Université de Genève30 Quai Ernest-Ansermet1211 GenèveSwitzerland
| | - Xin Xu
- Shanghai Key Laboratory of Molecular Catalysis and Innovation Materials, Collaborative Innovation Centre of Chemistry for Energy Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China.
| | - Weitao Yang
- Department of Chemistry and Physics, Duke University, Durham, NC 27516, USA.
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25
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Li JP, Dou LJ, Mu WH. Electronic and Steric Control of Rates and Selectivities in Rhodium-Catalyzed [2+2+2] Cycloadditions for Constructing Fused Tricyclic Hydronaphthofurans: A Density Functional Theory Study. J Org Chem 2022; 87:16328-16342. [DOI: 10.1021/acs.joc.2c01937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Jiang-Ping Li
- Faculty of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming 650092, China
| | - Li-Juan Dou
- Faculty of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming 650092, China
| | - Wei-Hua Mu
- Faculty of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming 650092, China
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26
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Tan S, Wang Y, Zhang IY, Xu X. Assessment of advanced xDH@B3LYP methods in describing various potential energy curves driven by π- π, CH/ π, and SH/ π non-bonded interactions. CHINESE J CHEM PHYS 2022. [DOI: 10.1063/1674-0068/cjcp2206098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Accurate description of potential energy curves driven by non-bonded interactions remains a great challenge for pure density functional approximations (DFAs). It is because the R−6 decay behavior of dispersion cannot be intrinsically captured by the (semi)-local ingredients and the exact-exchange used in the popular hybrid DFAs. Overemphasizing the accuracy on the equilibrium region for the functional construction would likely deteriorate the overall performance on the other regions of potential energy surfaces. In consequence, the empirical dispersion correction becomes the standard component in DFAs to treat the non-bonded interactions. In this Letter, we demonstrate that without the use of empirical dispersion correction, doubly hybrid approximations, in particular two recently proposed revXYG3 and XYG7 functionals, hold the promise to have a balanced description of non-bonded interactions on the whole potential energy curves for several prototypes of π- π, CH/ π, and SH/ π interactions. The error of revXYG3 and XYG7 for non-bonded interactions is around 0.1 kcal/mol, and their potential energy curves almost coincide with the accurate CCSD(T)/CBS curves.
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Affiliation(s)
- Shiqian Tan
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Yizhen Wang
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Igor Ying Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China
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27
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Nandeshwar M, Tarannum I, Kumar Singh S, Prabusankar G. Antimony(III)-selenium complexes with synergetic effect between Sb Se bond and Sb⋯π interactions. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.116069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Pentacoordinate Carbon Atoms in a Ferrocene Dication Derivative—[Fe(Si2-η5-C5H2)2]2+. CHEMISTRY 2022. [DOI: 10.3390/chemistry4040074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Pentacoordinate carbon atoms are theoretically predicted here in a ferrocene dication derivative in the eclipsed-(1; C2v), gauche-(2; C2) and staggered-[Fe(Si2-η5-C5H2)2]2+(3; C2h) forms for the first time. Energetically, the relative energy gaps for 2 and 3 range from −3.06 to 16.74 and −2.78 to 40.34 kJ mol−1, respectively, when compared to the singlet electronic state of 1 at different levels. The planar tetracoordinate carbon (ptC) atom in the ligand Si2C5H2 becomes a pentacoordinate carbon upon complexation. The ligand with a ptC atom was predicted to be both a thermodynamically and kinetically stable molecule by some of us in our earlier theoretical works. Natural bond orbital and adaptive natural density partitioning analyses confirm the pentacoordinate nature of carbon in these three complexes (1–3). Although they are hypothetical at the moment, they support the idea of “hypercoordinate metallocenes” within organometallic chemistry. Moreover, ab initio molecular dynamics simulations carried out at 298 K temperature for 2000 fs suggest that these molecules are kinetically stable.
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29
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Bintrim SJ, Berkelbach TC, Ye HZ. Integral-Direct Hartree-Fock and Møller-Plesset Perturbation Theory for Periodic Systems with Density Fitting: Application to the Benzene Crystal. J Chem Theory Comput 2022; 18:5374-5381. [PMID: 35969856 DOI: 10.1021/acs.jctc.2c00640] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an algorithm and implementation of integral-direct, density-fitted Hartree-Fock (HF) and second-order Møller-Plesset perturbation theory (MP2) for periodic systems. The new code eliminates the formerly prohibitive storage requirements and allows us to study systems 1 order of magnitude larger than before at the periodic MP2 level. We demonstrate the significance of the development by studying the benzene crystal in both the thermodynamic limit and the complete basis set limit, for which we predict an MP2 cohesive energy of -72.8 kJ/mol, which is about 10-15 kJ/mol larger in magnitude than all previously reported MP2 calculations. Compared to the best theoretical estimate from literature, several modified MP2 models approach chemical accuracy in the predicted cohesive energy of the benzene crystal and hence may be promising cost-effective choices for future applications on molecular crystals.
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Affiliation(s)
- Sylvia J Bintrim
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Timothy C Berkelbach
- Department of Chemistry, Columbia University, New York, New York 10027, United States.,Center for Computational Quantum Physics, Flatiron Institute, New York, New York 10010, United States
| | - Hong-Zhou Ye
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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30
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Santra G, Calinsky R, Martin JML. Benefits of Range-Separated Hybrid and Double-Hybrid Functionals for a Large and Diverse Data Set of Reaction Energies and Barrier Heights. J Phys Chem A 2022; 126:5492-5505. [PMID: 35930677 PMCID: PMC9393870 DOI: 10.1021/acs.jpca.2c03922] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
To better understand the thermochemical kinetics and
mechanism
of a specific chemical reaction, an accurate estimation of barrier
heights (forward and reverse) and reaction energies is vital. Because
of the large size of reactants and transition state structures involved
in real-life mechanistic studies (e.g., enzymatically catalyzed reactions),
density functional theory remains the workhorse for such calculations.
In this paper, we have assessed the performance of 91 density functionals
for modeling the reaction energies and barrier heights on a large
and chemically diverse data set (BH9) composed of 449 organic chemistry
reactions. We have shown that range-separated hybrid functionals perform
better than the global hybrids for BH9 barrier heights and reaction
energies. Except for the PBE-based range-separated nonempirical double
hybrids, range separation of the exchange term helps improve the performance
for barrier heights and reaction energies. The 16-parameter Berkeley
double hybrid, ωB97M(2), performs remarkably well for both properties.
However, our minimally empirical range-separated double hybrid functionals
offer marginally better accuracy than ωB97M(2) for BH9 barrier
heights and reaction energies.
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Affiliation(s)
- Golokesh Santra
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Rivka Calinsky
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Jan M L Martin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
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31
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Unexpected steric hindrance failure in the gas phase F - + (CH 3) 3CI S N2 reaction. Nat Commun 2022; 13:4427. [PMID: 35907925 PMCID: PMC9338938 DOI: 10.1038/s41467-022-32191-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Base-induced elimination (E2) and bimolecular nucleophilic substitution (SN2) reactions are of significant importance in physical organic chemistry. The textbook example of the retardation of SN2 reactivity by bulky alkyl substitution is widely accepted based on the static analysis of molecular structure and steric environment. However, the direct dynamical evidence of the steric hindrance of SN2 from experiment or theory remains rare. Here, we report an unprecedented full-dimensional (39-dimensional) machine learning-based potential energy surface for the 15-atom F− + (CH3)3CI reaction, facilitating the reliable and efficient reaction dynamics simulations that can reproduce well the experimental outcomes and examine associated atomic-molecular level mechanisms. Moreover, we found surprisingly high “intrinsic” reactivity of SN2 when the E2 pathway is completely blocked, indicating the reaction that intends to proceed via E2 transits to SN2 instead, due to a shared pre-reaction minimum. This finding indicates that the competing factor of E2 but not the steric hindrance determines the small reactivity of SN2 for the F− + (CH3)3CI reaction. Our study provides new insight into the dynamical origin that determines the intrinsic reactivity in gas-phase organic chemistry. Base-induced elimination (E2) and bimolecular nucleophilic substitution (SN2) are of significant importance in physical organic chemistry. Here, the authors show that the competing factor of E2 as opposed to steric hindrance determines the low reactivity of SN2 in the F− + (CH3)3CI reaction.
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32
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Gas- and liquid-phase ozonolysis of ethylene, butadiene, and perfluoro-olefins: solvation and the cage effect. MONATSHEFTE FUR CHEMIE 2022. [DOI: 10.1007/s00706-022-02946-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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33
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Synthesis, X-ray crystal structure, Hirshfeld analysis and computational investigation of bis(methylthio)acrylonitrile with antimicrobial and docking evaluation. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132793] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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34
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Abdel Gawad S, Mansour S, El-Baradie B, El-Mekawey F. Studies on spectro photophysical properties of PBBO-laser dye. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Bryenton KR, Adeleke AA, Dale SG, Johnson ER. Delocalization error: The greatest outstanding challenge in density‐functional theory. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kyle R. Bryenton
- Department of Physics and Atmospheric Science Dalhousie University Halifax Nova Scotia Canada
| | | | - Stephen G. Dale
- Queensland Micro‐ and Nanotechnology Centre Griffith University Nathan Queensland Australia
| | - Erin R. Johnson
- Department of Physics and Atmospheric Science Dalhousie University Halifax Nova Scotia Canada
- Department of Chemistry Dalhousie University Halifax Nova Scotia Canada
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36
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Yan W, Xu X. Analytic Gradients for the Long-Range-Corrected XYG3 Type of Doubly Hybrid Density Functionals: Theory, Implementation, and Assessment. J Phys Chem A 2022; 126:3937-3946. [PMID: 35686854 DOI: 10.1021/acs.jpca.2c01962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An analytic gradient algorithm for the long-range-corrected (lrc-) XYG3 type of doubly hybrid functionals has been derived and implemented. Due to the introduction of a long-range second-order perturbation (lrPT2) as the correction, the Z-vector equations need to be modified, where the construction of a unique total Lagrangian of the method is required. Geometry optimizations using lrc-XYG3 and lrc-XYGJ-OS have then been applied to the A21 data set that consists of 21 noncovalently interacting systems with CCSD(T) reference data for structures, in order to testify the idea of introducing lrPT2 for a better description of intermolecular interactions. While lrc-XYG3 was observed to offer a better description in dispersion-dominant systems as compared to the XYG3 functional, lrc-XYGJ-OS stands out with an overall better balanced performance in reproducing intermolecular geometries.
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Affiliation(s)
- Wenjie Yan
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
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37
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Lu X, Li L, Zhang X, Fu B, Xu X, Zhang DH. Dynamical Effects of S N2 Reactivity Suppression by Microsolvation: Dynamics Simulations of the F -(H 2O) + CH 3I Reaction on a 21-Dimensional Potential Energy Surface. J Phys Chem Lett 2022; 13:5253-5259. [PMID: 35674277 DOI: 10.1021/acs.jpclett.2c01323] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A comparison of atomistic dynamics between microsolvated and unsolvated reactions can expose the precise role of solvent molecules and thus provide deep insight into how solvation influences chemical reactions. Here we developed the first full-dimensional analytical potential energy surface of the F-(H2O) + CH3I reaction, which facilitates the efficient dynamics simulations on a quantitatively accurate level. The computed SN2 reactivity suppression ratio of the monosolvated F-(H2O) + CH3I reaction relative to the unsolvated F- + CH3I reaction as a function of collision energy first increases and then decreases steadily, forming an inverted-V shape, due to the combined dynamical effects of interaction time, steric hindrance, and collision-induced dehydration. Moreover, further analysis reveals that the steric effect of the F-(H2O) + CH3I reaction resulting from the single water molecule is manifested mainly in dragging the F- anion away from the central C atom, rather than shielding F- from C. Our study shows there is great potential in rigorously studying the role of the solvent in more complicated reactions.
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Affiliation(s)
- Xiaoxiao Lu
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lulu Li
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xiaoren Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Bina Fu
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xin Xu
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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38
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Yan W, Xu X. Accurate Prediction of Nuclear Magnetic Resonance Parameters via the XYG3 Type of Doubly Hybrid Density Functionals. J Chem Theory Comput 2022; 18:2931-2946. [PMID: 35467852 DOI: 10.1021/acs.jctc.2c00055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful and versatile tools in elucidating molecular structures. To eliminate ambiguities of experimental assignments, accurate calculations of NMR spectra are of great importance. Here, a method for theoretical evaluation of the NMR shielding constants by analytic derivatives using gauge including atomic orbitals (GIAO) has been implemented for the XYG3 type of doubly hybrid density functionals (xDH), namely, the GIAO-xDH method. Benchmark calculations on shielding constants and chemical shifts demonstrate the remarkable accuracy of the GIAO-xDH method, compared to the accurate CCSD(T) references. It is shown here that the XYGJ-OS functional is able to give a mean absolute deviation (MAD) of ∼3.0 ppm in the calculated shielding constants for 13C, 15N, 17O, 19F, while both XYGJ-OS and xDH-PBE0 functionals are able to provide a satisfactory estimation of chemical shifts with MADs of ∼0.03 and 1.0 ppm for 1H and 13C, respectively. The basis set influence upon the method has been examined and a computational scheme considering both accuracy and efficiency has been proposed and tested to predict the experimental 13C chemical shifts of five medium-sized natural product molecules, yielding a MAD of ∼1.0 ppm, which demonstrates the practical feasibility of the GIAO-xDH method.
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Affiliation(s)
- Wenjie Yan
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
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39
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Sim E, Song S, Vuckovic S, Burke K. Improving Results by Improving Densities: Density-Corrected Density Functional Theory. J Am Chem Soc 2022; 144:6625-6639. [PMID: 35380807 DOI: 10.1021/jacs.1c11506] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Density functional theory (DFT) calculations have become widespread in both chemistry and materials, because they usually provide useful accuracy at much lower computational cost than wavefunction-based methods. All practical DFT calculations require an approximation to the unknown exchange-correlation energy, which is then used self-consistently in the Kohn-Sham scheme to produce an approximate energy from an approximate density. Density-corrected DFT is simply the study of the relative contributions to the total energy error. In the vast majority of DFT calculations, the error due to the approximate density is negligible. But with certain classes of functionals applied to certain classes of problems, the density error is sufficiently large as to contribute to the energy noticeably, and its removal leads to much better results. These problems include reaction barriers, torsional barriers involving π-conjugation, halogen bonds, radicals and anions, most stretched bonds, etc. In all such cases, use of a more accurate density significantly improves performance, and often the simple expedient of using the Hartree-Fock density is enough. This Perspective explains what DC-DFT is, where it is likely to improve results, and how DC-DFT can produce more accurate functionals. We also outline challenges and prospects for the field.
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Affiliation(s)
- Eunji Sim
- Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 03722, Korea
| | - Suhwan Song
- Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 03722, Korea
| | - Stefan Vuckovic
- Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni,Campus Unisalento, 73100 Lecce, Italy.,Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Kieron Burke
- Departments of Chemistry and of Physics, University of California, Irvine, California 92697, United States
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40
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Wei L, Chen Y, Liu J, Rao L, Ren Y, Xu X, Wan J. Cov_DOX: A Method for Structure Prediction of Covalent Protein-Ligand Bindings. J Med Chem 2022; 65:5528-5538. [PMID: 35353519 DOI: 10.1021/acs.jmedchem.1c02007] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A handful of molecular docking tools have been extended to enable a covalent docking. However, all of them face the challenge brought by the covalent bond between proteins and ligands. Many covalent drug design scenarios still heavily rely on demanding crystallographic experiments for accurate binding structures. Aiming at filling the gap between covalent dockings and crystallographic experiments, we develop and validate a hybrid method, dubbed as Cov_DOX, in this work. Cov_DOX achieves an overall success rate of 81% with RMSD < 2 Å for the Top 1 pose prediction in the validation against a test set including 405 crystal structures for covalent protein-ligand complexes, covering various types of the warhead chemistry and receptors. Such accuracy is not far from the much more demanding crystallographic experiments, in sharp contrast to the performance of the covalent docking front runners (success rate: 40-60%).
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Affiliation(s)
- Lin Wei
- Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 43009, China
| | - Yaru Chen
- Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 43009, China
| | - Jiaqi Liu
- Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 43009, China
| | - Li Rao
- Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 43009, China
| | - Yanliang Ren
- Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 43009, China
| | - Xin Xu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education (MOE) Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, People's Republic of China
| | - Jian Wan
- Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 43009, China
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41
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Ludeña EV, Torres FJ, Rincón L. A general justification for hybrid functionals in DFT by means of linear response theory. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:194004. [PMID: 35144254 DOI: 10.1088/1361-648x/ac53d9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
In the present work, resorting to linear response theory, we examine the plausibility of postulating Kohn-Sham (KS)-type equations which contain, by definition, an effective hybrid potential made up by some arbitrary mixture of local and non-local terms. In this way a general justification for the construction of hybrid functionals is provided without resorting to arguments based on the adiabatic connection, the generalized KS theory or the Levy's constrained search (or its variations). In particular, we examine the cases of single-hybrid functionals, derived from non-local exchange and of double-hybrid functionals, emerging from non-local second-order expressions obtained from the KS perturbation theory. A further generalization for higher-order hybrid functionals is also included.
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Affiliation(s)
- Eduardo V Ludeña
- Laboratorio de Físico-Química Teórica de Materiales, Centro de Química, IVIC, Apartado 21827, Caracas 1020 A, Venezuela
| | - F Javier Torres
- Grupo de Química Computacional y Teórica (QCT-UR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Quito, Ecuador
| | - Luis Rincón
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Quito, Ecuador
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42
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Wang J, Zhang D, Xu RX, Yam C, Chen G, Zheng X. Improving Density Functional Prediction of Molecular Thermochemical Properties with a Machine-Learning-Corrected Generalized Gradient Approximation. J Phys Chem A 2022; 126:970-978. [PMID: 35113552 DOI: 10.1021/acs.jpca.1c10491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The past decade has seen an increasing interest in designing sophisticated density functional approximations (DFAs) by integrating the power of machine learning (ML) techniques. However, application of the ML-based DFAs is often confined to simple model systems. In this work, we construct an ML correction to the widely used Perdew-Burke-Ernzerhof (PBE) functional by establishing a semilocal mapping from the electron density and reduced gradient to the exchange-correlation energy density. The resulting ML-corrected PBE is immediately applicable to any real molecule and yields significantly improved heats of formation while preserving the accuracy for other thermochemical and kinetic properties. This work highlights the prospect of combining the power of data-driven ML methods with physics-inspired derivations for reaching the heaven of chemical accuracy.
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Affiliation(s)
- JingChun Wang
- Hefei National Laboratory for Physical Sciences at the Microscale & Synergetic Innovation Center of Quantum Information and Quantum Physics & CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - DaDi Zhang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Rui-Xue Xu
- Hefei National Laboratory for Physical Sciences at the Microscale & Synergetic Innovation Center of Quantum Information and Quantum Physics & CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - ChiYung Yam
- Beijing Computational Science Research Center, Beijing 100193, China
| | - GuanHua Chen
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiao Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale & Synergetic Innovation Center of Quantum Information and Quantum Physics & CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, Anhui 230026, China
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43
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Mei Y, Yu J, Chen Z, Su NQ, Yang W. LibSC: Library for Scaling Correction Methods in Density Functional Theory. J Chem Theory Comput 2022; 18:840-850. [DOI: 10.1021/acs.jctc.1c01058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuncai Mei
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Jincheng Yu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Zehua Chen
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Neil Qiang Su
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Physics, Duke University, Durham, North Carolina 27708, United States
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44
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Sancho-García JC, Brémond E, Ricci G, Pérez-Jiménez AJ, Olivier Y, Adamo C. Violation of Hund’s rule in molecules: Predicting the excited-state energy inversion by TD-DFT with double-hybrid methods. J Chem Phys 2022; 156:034105. [DOI: 10.1063/5.0076545] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- J. C. Sancho-García
- Department of Physical Chemistry, University of Alicante, E-03080 Alicante, Spain
| | - E. Brémond
- Université de Paris, ITODYS, CNRS, F-75006 Paris, France
| | - G. Ricci
- Laboratory for Computational Modeling of Functional Materials, Namur Institute of Structured Matter, Université de Namur, Rue de Bruxelles, B-5000 Namur, Belgium
| | - A. J. Pérez-Jiménez
- Department of Physical Chemistry, University of Alicante, E-03080 Alicante, Spain
| | - Y. Olivier
- Laboratory for Computational Modeling of Functional Materials, Namur Institute of Structured Matter, Université de Namur, Rue de Bruxelles, B-5000 Namur, Belgium
| | - C. Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Life and Health Sciences (i-CLeHS), FRE 2027, F-75005 Paris, France
- Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris, France
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45
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Mester D, Kállay M. Accurate Spectral Properties within Double-Hybrid Density Functional Theory: A Spin-Scaled Range-Separated Second-Order Algebraic-Diagrammatic Construction-Based Approach. J Chem Theory Comput 2022; 18:865-882. [PMID: 35023739 PMCID: PMC8830052 DOI: 10.1021/acs.jctc.1c01100] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Our second-order algebraic-diagrammatic construction [ADC(2)]-based double-hybrid (DH) ansatz (J. Chem. Theory Comput. 2019, 15, 4440. DOI: 10.1021/acs.jctc.9b00391) is combined with range-separation techniques. In the present scheme, both the exchange and the correlation contributions are range-separated, while spin-scaling approaches are also applied. The new methods are thoroughly tested for the most popular benchmark sets including 250 singlet and 156 triplet excitations, as well as 80 oscillator strengths. It is demonstrated that the range separation for the correlation contributions is highly recommended for both the genuine and the ADC(2)-based DH approaches. Our results show that the latter scheme slightly but consistently outperforms the former one for single excitation dominated transitions. Furthermore, states with larger fractions of double excitations are assessed as well, and challenging charge-transfer excitations are also discussed, where the recently proposed spin-scaled long-range corrected DHs fail. The suggested iterative fourth-power scaling RS-PBE-P86/SOS-ADC(2) method, using only three adjustable parameters, provides the most robust and accurate excitation energies within the DH theory. In addition, the relative error of the oscillator strengths is reduced by 65% compared to the best genuine DH functionals.
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Affiliation(s)
- Dávid Mester
- 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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46
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Theoretical Description of Water from Single-Molecule to Condensed Phase: a Review of Recent Progress on Potential Energy Surfaces and Molecular Dynamics. CHINESE J CHEM PHYS 2022. [DOI: 10.1063/1674-0068/cjcp2201005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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47
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Morán-González L, Besora M, Maseras F. Seeking the Optimal Descriptor for S N2 Reactions through Statistical Analysis of Density Functional Theory Results. J Org Chem 2021; 87:363-372. [PMID: 34935370 DOI: 10.1021/acs.joc.1c02387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bimolecular nucleophilic substitution is one of the fundamental reactions in organic chemistry, yet there is still knowledge to be gained on the role of the nucleophile and the substrate. A statistical treatment of over 600 density functional theory (DFT)-computed barriers for bimolecular nucleophilic substitution at methyl derivatives (SN2@C) leads to the identification of numerical descriptors that best represent the entering and leaving ability of 26 different nucleophiles. The treatment is based on singular value decomposition (SVD) of a matrix of computed energy barriers. The current work represents the extension to a problem of reactivity of the hidden descriptor methodology that we had previously developed for the thermodynamic problem of bond dissociation energies in transition-metal complexes. The analysis of the results shows that a single descriptor is sufficient. This hidden descriptor has different values for nucleophilic and leaving abilities and, contrary to expectation, does not correlate especially well with either frontier molecular orbital descriptors or solvation descriptors. In contrast, it correlates with other thermodynamic and geometric parameters. This statistical procedure can be in principle extended to additional chemical fragments and other reactions.
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Affiliation(s)
- Lucía Morán-González
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007 Tarragona, Catalonia, Spain
| | - Maria Besora
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, c/Marcel·lí Domingo s/n, 43007 Tarragona, Catalonia, Spain
| | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007 Tarragona, Catalonia, Spain
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48
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Gu Y, Xu X. Symmetry Dilemma of Doubly Hybrid Density Functionals for Equilibrium Molecular Property Calculations. J Chem Theory Comput 2021; 17:7745-7752. [PMID: 34839668 DOI: 10.1021/acs.jctc.1c00990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In electronic structure theory, when an approximate wavefunction tends to artifactually break the symmetry of the exact Hamiltonian, the corresponding method is referred to as having a "symmetry dilemma" problem. Such types of artifacts were often reported when Hartree-Fock (HF) and the low-level post-HF methods were used, while the traditional Kohn-Sham density functional theory (KS-DFT) methods were usually found to be more resistant to this breakdown. In this work, we present a systematic study on the reliability of the doubly hybrid (DH) DFT methods for several violable cases. Almost all the commonly used B2PLYP-type (bDH) functionals are shown to have a severe "symmetry dilemma" problem and yield dramatically unreliable molecular properties, such as dipole moment, vibrational frequency, and static polarizability at the equilibrium geometry. A one-parameter bDH functional model study demonstrates that such a problem is a combined effect of the inappropriate portion of the HF exchange (over 50%) for the self-consistent field (SCF) calculation and the augmentation of the second-order perturbative contribution. It is remarkable that the XYG3-type (xDH) functionals show a good capability to resist the artifactual symmetry breaking and yield reliable molecular properties when the same critical cases are calculated. In the xDH, there are two functionals of different purposes, namely, the SCF functional and the energy functional, which have different amounts of the HF exchange and different portions of the correlation contributions. The success of the xDHs can be attributed to this flexibility in xDH construction to avoid using an improperly large portion of the HF exchange in the SCF functional. The insights gained in this work are of significance for the development of an improved DH functional.
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Affiliation(s)
- Yonghao Gu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai 200433, China
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49
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Wang P, Shu C, Ye H, Biczysko M. Structural and Energetic Properties of Amino Acids and Peptides Benchmarked by Accurate Theoretical and Experimental Data. J Phys Chem A 2021; 125:9826-9837. [PMID: 34752094 DOI: 10.1021/acs.jpca.1c06504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Structural, energetic, and spectroscopic data derived in this work aim at the setup of an "experimentally validated" database for amino acids and polypeptides conformers. First, the "cheap" composite scheme (ChS, CCSD(T)/(CBS+CV)MP2) is tested for evaluation of conformational energies of all eight stable conformers of glycine, by comparing to the more accurate CCSD(T)/CBS+CV computations (Phys. Chem. Chem. Phys. 2013, 15, 10094-10111 and J Mol. Model. 2020, 26, 129). The recently proposed jun-ChS (J. Chem. Theory and Comput. 2020, 16, 988-1006), employing the jun-cc-pVnZ basis set family for CCSD(T) computations and CBS extrapolation, yields conformational energies accurate to 0.2 kJ·mol-1, at reduced computational cost with respect to aug-ChS employing aug-cc-pVnZ basis sets. The jun-ChS composite scheme is further applied to derive conformational energies for three dipeptide analogues Ac-Gly-NH2, Ac-Ala-NH2, and Gly-Gly. Finally, dipeptide conformational energies and semiexperimental equilibrium rotational constants along with the CCSD(T)/(CBS+CV)MP2 structural parameters (J. Phys. Chem. Lett. 2014, 5, 534-540) stand as the reference for benchmarking of selected density functional methodologies. The double-hybrid functionals B2-PLYP-D3(BJ) and DSD-PBEP86, perform best for structural and energetic characterization of all dipeptide analogues. From hybrid functionals CAM-B3LYP-D3(BJ) and ωB97X-D3(BJ) represent promising methods applicable for larger peptide-based systems for which computations with double-hybrid functionals are not feasible.
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Affiliation(s)
- Ping Wang
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Chong Shu
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Hexu Ye
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
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50
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Yang S, Zhang Z, Zhang DH. A full-dimensional ab initio potential energy and dipole moment surfaces for (NH 3) 2. J Chem Phys 2021; 155:164306. [PMID: 34717358 DOI: 10.1063/5.0072063] [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
A full-dimensional ab initio potential energy surface (PES) and dipole moment surface (DMS) for the ammonia dimer (NH3)2 are reported. The database of the PES consists of 27 736 ab initio energy points and all of these points were calculated at the UCCSD(T)-F12a/AVTZ level. The PES was fitted by using the fundamental invariant neural network (FI-NN) method that satisfies the permutational symmetry of identical atoms, and the root mean square fitting error for the PES is very small as low as 0.562 meV. The geometries for the (NH3)2 DMS are the same as those used for the PES and are calculated at the XYG3/AVTZ level. This PES can describe a variety of internal floppy motions, including all kinds of vibrational modes no matter intermolecular or intramolecular. The CCSD(T)-PES can dissociate correctly to two NH3 monomers, with De = 1135.55 cm-1 (13.58 kJ/mol) which agrees accurately with the 13.5 ± 0.3 kJ/mol predicted by previous work.
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Affiliation(s)
- Shuo Yang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China
| | - Zhaojun Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China
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