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Pederson JP, McDaniel JG. PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics. J Chem Phys 2024; 161:034103. [PMID: 39007371 DOI: 10.1063/5.0219851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
PyDFT-QMMM is a Python-based package for performing hybrid quantum mechanics/molecular mechanics (QM/MM) simulations at the density functional level of theory. The program is designed to treat short-range and long-range interactions through user-specified combinations of electrostatic and mechanical embedding procedures within periodic simulation domains, providing necessary interfaces to external quantum chemistry and molecular dynamics software. To enable direct embedding of long-range electrostatics in periodic systems, we have derived and implemented force terms for our previously described QM/MM/PME approach [Pederson and McDaniel, J. Chem. Phys. 156, 174105 (2022)]. Communication with external software packages Psi4 and OpenMM is facilitated through Python application programming interfaces (APIs). The core library contains basic utilities for running QM/MM molecular dynamics simulations, and plug-in entry-points are provided for users to implement custom energy/force calculation and integration routines, within an extensible architecture. The user interacts with PyDFT-QMMM primarily through its Python API, allowing for complex workflow development with Python scripting, for example, interfacing with PLUMED for free energy simulations. We provide benchmarks of forces and energy conservation for the QM/MM/PME and alternative QM/MM electrostatic embedding approaches. We further demonstrate a simple example use case for water solute in a water solvent system, for which radial distribution functions are computed from 100 ps QM/MM simulations; in this example, we highlight how the solvation structure is sensitive to different basis-set choices due to under- or over-polarization of the QM water molecule's electron density.
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Affiliation(s)
- John P Pederson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Jesse G McDaniel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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Bowling PE, Dasgupta S, Herbert JM. Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites. J Chem Inf Model 2024; 64:3912-3922. [PMID: 38648614 DOI: 10.1021/acs.jcim.4c00221] [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: 04/25/2024]
Abstract
In constructing finite models of enzyme active sites for quantum-chemical calculations, atoms at the periphery of the model must be constrained to prevent unphysical rearrangements during geometry relaxation. A simple fixed-atom or "coordinate-lock" approach is commonly employed but leads to undesirable artifacts in the form of small imaginary frequencies. These preclude evaluation of finite-temperature free-energy corrections, limiting thermochemical calculations to enthalpies only. Full-dimensional vibrational frequency calculations are possible by replacing the fixed-atom constraints with harmonic confining potentials. Here, we compare that approach to an alternative strategy in which fixed-atom contributions to the Hessian are simply omitted. While the latter strategy does eliminate imaginary frequencies, it tends to underestimate both the zero-point energy and the vibrational entropy while introducing artificial rigidity. Harmonic confining potentials eliminate imaginary frequencies and provide a flexible means to construct active-site models that can be used in unconstrained geometry relaxations, affording better convergence of reaction energies and barrier heights with respect to the model size, as compared to models with fixed-atom constraints.
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Affiliation(s)
- Paige E Bowling
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, California 92093, United States
| | - John M Herbert
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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Nochebuena J, Liu S, Cisneros GA. Relative cooperativity in neutral and charged molecular clusters using QM/MM calculations. J Chem Phys 2024; 160:134301. [PMID: 38557841 DOI: 10.1063/5.0203020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
QM/MM methods have been used to study electronic structure properties and chemical reactivity in complex molecular systems where direct electronic structure calculations are not feasible. In our previous work, we showed that non-polarizable force fields, by design, describe intermolecular interactions through pairwise interactions, overlooking many-body interactions involving three or more particles. In contrast, polarizable force fields account partially for many-body effects through polarization, but still handle van der Waals and permanent electrostatic interactions pairwise. We showed that despite those limitations, polarizable and non-polarizable force fields can reproduce relative cooperativity achieved using density functional theory due to error compensation mechanisms. In this contribution, we assess the performance of QM/MM methods in reproducing these phenomena. Our study highlights the significance of the QM region size and force field choice in QM/MM calculations, emphasizing the importance of parameter validation to obtain accurate interaction energy predictions.
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Affiliation(s)
- Jorge Nochebuena
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - G Andrés Cisneros
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, USA
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, USA
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Zheng M, Li Y, Zhang Q, Wang W. Impacts of QM region sizes and conformation numbers on modelling enzyme reactions: a case study of polyethylene terephthalate hydrolase. Phys Chem Chem Phys 2023; 25:31596-31603. [PMID: 37917137 DOI: 10.1039/d3cp04519f] [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: 11/03/2023]
Abstract
A quantum mechanics/molecular mechanics (QM/MM) approach is a broadly used tool in computational enzymology. Treating the QM region with a high-level DFT method is one of the important branches. Here, taking leaf-branch compost cutinase-catalyzed polyethylene terephthalate depolymerization as an example, the convergence behavior of energy barriers as well as key structural and charge features with respect to the size of the QM region (up to 1000 atoms) is systematically investigated. BP86/6-31G(d)//CHARMM and M06-2X/6-311G(d,p)//CHARMM level of theories were applied for geometry optimizations and single-point energy calculations, respectively. Six independent enzyme conformations for all the four catalytic steps (steps (i)-(iv)) were considered. Most of the twenty-four cases show that at least 500 QM atoms are needed while only two rare cases show that ∼100 QM atoms are sufficient for convergence when only a single conformation was considered. This explains why most previous studies showed that 500 or more QM atoms are required while a few others showed that ∼100 QM atoms are sufficient for DFT/MM calculations. More importantly, average energy barriers and key structural/charge features from six conformations show an accelerated convergence than that in a single conformation. For instance, to reach energy barrier convergence (within 2.0 kcal mol-1) for step (ii), only ∼100 QM atoms are required if six conformations are considered while 500 or more QM atoms are needed with a single conformation. The convergence is accelerated to be more rapid if hundreds and thousands of conformations were considered, which aligns with previous findings that only several dozens of QM atoms are required for convergence with semi-empirical QM/MM MD simulations.
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Affiliation(s)
- Mingna Zheng
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China.
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China.
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China.
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China.
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Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
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Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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Godesi S, Nada H, Lee J, Kang JH, Kim SY, Choi Y, Lee K. Integration of Hybridization Strategies in Pyridine-Urea Scaffolds for Novel Anticancer Agents: Design, Synthesis, and Mechanistic Insights. Molecules 2023; 28:4952. [PMID: 37446614 DOI: 10.3390/molecules28134952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Annually, millions of new cancer cases are reported, leading to millions of deaths worldwide. Among the newly reported cases, breast and colon cancers prevail as the most frequently detected variations. To effectively counteract this rapid increase, the development of innovative therapies is crucial. Small molecules possessing pyridine and urea moieties have been reported in many of the currently available anticancer agents, especially VEGFR2 inhibitors. With this in mind, a rational design approach was employed to create hybrid small molecules combining urea and pyridine. These synthesized compounds underwent in vitro testing against breast and colon cancer cell lines, revealing potent submicromolar anticancer activity. Compound 8a, specifically, exhibited an impressive GI50 value of 0.06 μM against the MCF7 cancer cell line, while compound 8h displayed the highest cytotoxic activity against the HCT116 cell line, with a GI50 of 0.33 ± 0.042 μM. Notably, compounds 8a, 8h, and 8i demonstrated excellent safety profiles when tested on normal cells. Molecular docking, dynamic studies, and free energy calculations were employed to validate the affinity of these compounds as VEGFR2 inhibitors.
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Affiliation(s)
- Sreenivasulu Godesi
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Hossam Nada
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Badr University in Cairo, Cairo 11829, Egypt
| | - Joohan Lee
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Joon-Hee Kang
- Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Republic of Korea
| | - Soo-Youl Kim
- Division of Cancer Biology, Research Institute, National Cancer Center, Goyang 10408, Republic of Korea
| | - Yongseok Choi
- College of Biosciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Kyeong Lee
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea
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Kubař T, Elstner M, Cui Q. Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines. Annu Rev Biophys 2023; 52:525-551. [PMID: 36791746 PMCID: PMC10810093 DOI: 10.1146/annurev-biophys-111622-091140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods have become indispensable tools for the study of biomolecules. In this article, we briefly review the basic methodological details of QM/MM approaches and discuss their applications to various energy transduction problems in biomolecular machines, such as long-range proton transports, fast electron transfers, and mechanochemical coupling. We highlight the particular importance for these applications of balancing computational efficiency and accuracy. Using several recent examples, we illustrate the value and limitations of QM/MM methodologies for both ground and excited states, as well as strategies for calibrating them in specific applications. We conclude with brief comments on several areas that can benefit from further efforts to make QM/MM analyses more quantitative and applicable to increasingly complex biological problems.
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Affiliation(s)
- T Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany;
| | - M Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany;
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany;
| | - Q Cui
- Department of Chemistry, Boston University, Boston, Massachusetts, USA;
- Department of Physics, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
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Zlobin A, Belyaeva J, Golovin A. Challenges in Protein QM/MM Simulations with Intra-Backbone Link Atoms. J Chem Inf Model 2023; 63:546-560. [PMID: 36633836 DOI: 10.1021/acs.jcim.2c01071] [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: 01/13/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) simulations fuel discoveries in many fields of science including computational biochemistry and enzymology. Development of more convenient tools leads to an increase in the number of works in which mechanical insights into enzymes' mode of operation are obtained. Most commonly, these tools feature hydrogen-capping (link atom) approach to provide coupling between QM and MM subsystems across a covalent bond. Extensive studies were conducted to provide a solid foundation for the correctness of such an approach when a bond to a nonpolar MM atom is considered. However, not every task may be accomplished this way. Certain scenarios of using QM/MM in computational enzymology encourage or even necessitate the incorporation of backbone atoms into the QM region. Two out of three backbone atoms are polar, and in QM/MM with electrostatic embedding, a neighboring link atom will be hyperpolarized. Several schemes to mitigate this effect were previously proposed alongside a rigorous assessment of quantitative effects on model systems. However, it was not clear whether they may translate into qualitatively different results and how link atom hyperpolarization may manifest itself in a real-life enzymological scenario. Here, we show that the consequences of such an artifact may be severe and may completely overturn the conclusions drawn from the simulations. Our case advocates for the use of charge redistribution schemes whenever intra-backbone QM/MM boundaries are considered. Moreover, we addressed how different boundary types and charge redistribution schemes influence backbone dynamics. We showed that the results are heavily dependent on which boundary MM terms are retained, with charge alteration being of secondary importance. In the worst case, only three intra-backbone boundaries may be used with relative confidence in the adequacy of resulting simulations, irrespective of the hyperpolarization mitigation scheme. Thus, advances in the field are certainly needed to fuel new discoveries. As of now, we believe that issues raised in this work might encourage authors in the field to report what boundaries, boundary MM terms, and charge redistribution schemes they are using, so their results may be correctly interpreted.
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Affiliation(s)
- Alexander Zlobin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Julia Belyaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Andrey Golovin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
- Sirius University of Science and Technology, 354340 Sochi, Russia
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Jiang Y, Stull SL, Shao Q, Yang ZJ. Convergence in determining enzyme functional descriptors across Kemp eliminase variants. ELECTRONIC STRUCTURE (BRISTOL, ENGLAND) 2022; 4:044007. [PMID: 37425623 PMCID: PMC10327861 DOI: 10.1088/2516-1075/acad51] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Molecular simulations have been extensively employed to accelerate biocatalytic discoveries. Enzyme functional descriptors derived from molecular simulations have been leveraged to guide the search for beneficial enzyme mutants. However, the ideal active-site region size for computing the descriptors over multiple enzyme variants remains untested. Here, we conducted convergence tests for dynamics-derived and electrostatic descriptors on 18 Kemp eliminase variants across six active-site regions with various boundary distances to the substrate. The tested descriptors include the root-mean-square deviation of the active-site region, the solvent accessible surface area ratio between the substrate and active site, and the projection of the electric field (EF) on the breaking C-H bond. All descriptors were evaluated using molecular mechanics methods. To understand the effects of electronic structure, the EF was also evaluated using quantum mechanics/molecular mechanics methods. The descriptor values were computed for 18 Kemp eliminase variants. Spearman correlation matrices were used to determine the region size condition under which further expansion of the region boundary does not substantially change the ranking of descriptor values. We observed that protein dynamics-derived descriptors, including RMSDactive_site and SASAratio, converge at a distance cutoff of 5 Å from the substrate. The electrostatic descriptor, EFC-H, converges at 6 Å using molecular mechanics methods with truncated enzyme models and 4 Å using quantum mechanics/molecular mechanics methods with whole enzyme model. This study serves as a future reference to determine descriptors for predictive modeling of enzyme engineering.
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Affiliation(s)
- Yaoyukun Jiang
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
| | - Sebastian L Stull
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
| | - Qianzhen Shao
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
| | - Zhongyue J Yang
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, United States of America
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, United States of America
- Data Science Institute, Vanderbilt University, Nashville, TN 37235, United States of America
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, United States of America
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Theoretical studies of metal-organic frameworks: Calculation methods and applications in catalysis, gas separation, and energy storage. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214670] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Chen J, Harper JB, Ho J. Improving the Accuracy of Quantum Mechanics/Molecular Mechanics (QM/MM) Models with Polarized Fragment Charges. J Chem Theory Comput 2022; 18:5607-5617. [PMID: 35952004 DOI: 10.1021/acs.jctc.2c00491] [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
This paper introduces an economical approach for improving the accuracy and convergence of quantum mechanics/molecular mechanics (QM/MM) models. The approach is tested on a series of neutral and charged amino acids embedded in a 160-water cluster, where their intramolecular proton transfer energies (neutral amino acid → zwitterionic amino acid) were previously obtained at the ωB97X-D/6-31G(d) level of theory. When the charges on the MM atoms were replaced with those obtained at the same QM level of theory used to treat the QM atoms, this significantly improved the accuracy and convergence of the QM/MM models. In particular, the QM/MM model converged to within 1.4 kcal mol-1 of directly calculated DFT energies for smaller (by as many as 20 waters) QM regions. The use of atomic charges obtained from the natural population analysis yielded the most significant improvement, while other charge schemes such as Mulliken, electrostatic potential, or CM5 led to poorer outcomes. It is further demonstrated that the QM atomic charges can be accurately estimated in a highly efficient manner using an iterative fragmentation approach based on the moving-domain QM/MM method. Similar observations were made when the approach was used to predict the barrier of an SN2 reaction. Thus, the use of QM-quality atomic charges on MM atoms represents a simple and easy-to-implement strategy for improving the accuracy of QM/MM models.
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Affiliation(s)
- Junbo Chen
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jason B Harper
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Junming Ho
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
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