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Wang S, Hensley AJ. Rotational Symmetry Effects on Multibody Lateral Interactions between Co-Adsorbates at Heterogeneous Interfaces. ACS PHYSICAL CHEMISTRY AU 2024; 4:328-335. [PMID: 39069980 PMCID: PMC11274285 DOI: 10.1021/acsphyschemau.4c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 07/30/2024]
Abstract
Heterogeneous interfaces are critical in a wide range of applications, and their material properties can be tuned via changes in the coverage and configuration of chemical adsorbates. However, the tunability of such adlayers is limited by a lack of knowledge surrounding the impact of adsorbate internal structure and rotational symmetry on lateral interactions between coadsorbates. Using density functional theory (DFT) and cluster expansions, we systematically determine the impacts of rotational symmetry on lateral interactions between coadsorbates as a function of DFT functional, adsorbate type, metal type, and cluster configuration. Results indicate that the rotational symmetry effects can be nearly exclusively partitioned into the shortest 2-body clusters. By electronic analysis, the nature and strength of such effects on the lateral interactions are attributed to a balance of repulsive and attractive electrostatic interactions that are dependent on the adsorbate and metal types. Taken together, our characterization of the impacts of adsorbate internal structure and rotational symmetry on lateral interactions enables improved accuracy within multiscale modeling of multibody adsorbates at heterogeneous interfaces.
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Affiliation(s)
- Shuqiao Wang
- Department of Chemical Engineering
and Materials Science, Stevens Institute
of Technology, Hoboken, New Jersey 07030 United States
| | - Alyssa J.R. Hensley
- Department of Chemical Engineering
and Materials Science, Stevens Institute
of Technology, Hoboken, New Jersey 07030 United States
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2
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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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3
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Kao YC, Wang YM, Yeh JY, Li SC, Wu KCW, Lin LC, Li YP. Tailoring parameters for QM/MM simulations: accurate modeling of adsorption and catalysis in zirconium-based metal-organic frameworks. Phys Chem Chem Phys 2024. [PMID: 39015995 DOI: 10.1039/d4cp00681j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) simulations offer an efficient way to model reactions occurring in complex environments. This study introduces a specialized set of charge and Lennard-Jones parameters tailored for electrostatically embedded QM/MM calculations, aiming to accurately model both adsorption processes and catalytic reactions in zirconium-based metal-organic frameworks (Zr-MOFs). To validate our approach, we compare adsorption energies derived from QM/MM simulations against experimental results and Monte Carlo simulation outcomes. The developed parameters showcase the ability of QM/MM simulations to represent long-range electrostatic and van der Waals interactions faithfully. This capability is evidenced by the prediction of adsorption energies with a low root mean square error of 1.1 kcal mol-1 across a wide range of adsorbates. The practical applicability of our QM/MM model is further illustrated through the study of glucose isomerization and epimerization reactions catalyzed by two structurally distinct Zr-MOF catalysts, UiO-66 and MOF-808. Our QM/MM calculations closely align with experimental activation energies. Importantly, the parameter set introduced here is compatible with the widely used universal force field (UFF). Moreover, we thoroughly explore how the size of the cluster model and the choice of density functional theory (DFT) methodologies influence the simulation outcomes. This work provides an accurate and computationally efficient framework for modeling complex catalytic reactions within Zr-MOFs, contributing valuable insights into their mechanistic behaviors and facilitating further advancements in this dynamic area of research.
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Affiliation(s)
- Yu-Chi Kao
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
| | - Yi-Ming Wang
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
| | - Jyun-Yi Yeh
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
- International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Shih-Cheng Li
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
| | - Kevin C-W Wu
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
- International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
- Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-Li, Taoyuan, Taiwan
| | - Li-Chiang Lin
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Avenue, Columbus, OH, 43210-1350, USA
| | - Yi-Pei Li
- Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
- Taiwan International Graduate Program on Sustainable Chemical Science and Technology (TIGP-SCST), No. 128, Sec. 2, Academia Road, Taipei, 11529, Taiwan
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4
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Imamura K, Yokogawa D, Sato H. Recent developments and applications of reference interaction site model self-consistent field with constrained spatial electron density (RISM-SCF-cSED): A hybrid model of quantum chemistry and integral equation theory of molecular liquids. J Chem Phys 2024; 160:050901. [PMID: 38341702 DOI: 10.1063/5.0190116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/04/2024] [Indexed: 02/13/2024] Open
Abstract
The significance of solvent effects in electronic structure calculations has long been noted, and various methods have been developed to consider this effect. The reference interaction site model self-consistent field with constrained spatial electron density (RISM-SCF-cSED) is a hybrid model that combines the integral equation theory of molecular liquids with quantum chemistry. This method can consider the statistically convergent solvent distribution at a significantly lower cost than molecular dynamics simulations. Because the RISM theory explicitly considers the solvent structure, it performs well for systems where hydrogen bonds are formed between the solute and solvent molecules, which is a challenge for continuum solvent models. Taking advantage of being founded on the variational principle, theoretical developments have been made in calculating various properties and incorporating electron correlation effects. In this review, we organize the theoretical aspects of RISM-SCF-cSED and its distinctions from other hybrid methods involving integral equation theories. Furthermore, we carefully present its progress in terms of theoretical developments and recent applications.
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Affiliation(s)
- Kosuke Imamura
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Daisuke Yokogawa
- Graduate School of Arts and Science, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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Schnee P, Pleiss J, Jeltsch A. Approaching the catalytic mechanism of protein lysine methyltransferases by biochemical and simulation techniques. Crit Rev Biochem Mol Biol 2024; 59:20-68. [PMID: 38449437 DOI: 10.1080/10409238.2024.2318547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/10/2024] [Indexed: 03/08/2024]
Abstract
Protein lysine methyltransferases (PKMTs) transfer up to three methyl groups to the side chains of lysine residues in proteins and fulfill important regulatory functions by controlling protein stability, localization and protein/protein interactions. The methylation reactions are highly regulated, and aberrant methylation of proteins is associated with several types of diseases including neurologic disorders, cardiovascular diseases, and various types of cancer. This review describes novel insights into the catalytic machinery of various PKMTs achieved by the combined application of biochemical experiments and simulation approaches during the last years, focusing on clinically relevant and well-studied enzymes of this group like DOT1L, SMYD1-3, SET7/9, G9a/GLP, SETD2, SUV420H2, NSD1/2, different MLLs and EZH2. Biochemical experiments have unraveled many mechanistic features of PKMTs concerning their substrate and product specificity, processivity and the effects of somatic mutations observed in PKMTs in cancer cells. Structural data additionally provided information about the substrate recognition, enzyme-substrate complex formation, and allowed for simulations of the substrate peptide interaction and mechanism of PKMTs with atomistic resolution by molecular dynamics and hybrid quantum mechanics/molecular mechanics methods. These simulation technologies uncovered important mechanistic details of the PKMT reaction mechanism including the processes responsible for the deprotonation of the target lysine residue, essential conformational changes of the PKMT upon substrate binding, but also rationalized regulatory principles like PKMT autoinhibition. Further developments are discussed that could bring us closer to a mechanistic understanding of catalysis of this important class of enzymes in the near future. The results described here illustrate the power of the investigation of enzyme mechanisms by the combined application of biochemical experiments and simulation technologies.
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Affiliation(s)
- Philipp Schnee
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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6
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Imamura K, Yasuike T, Sato H. Open-boundary cluster model with a parameter-free complex absorbing potential. J Chem Phys 2024; 160:034103. [PMID: 38230813 DOI: 10.1063/5.0184571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/22/2023] [Indexed: 01/18/2024] Open
Abstract
In quantum chemical calculations of heterogeneous structures in solids, e.g., when an impurity is located on the surface, the conventional cluster model is insufficient to describe the electronic structure of substrates due to its finite size. The open-boundary cluster model (OCM) overcomes this problem by performing cluster calculations under the outgoing-wave boundary condition. In this method, a complex absorbing potential (CAP) is used to impose the boundary condition, but the CAP used in the previous studies required parameter optimization based on the complex variational principle. This study proposes and applies a parameter-free CAP to OCM calculations. This approach makes it possible to uniquely determine the band-specific CAP based on the surface Green's function theory. Using this CAP, we conducted OCM calculations of the tight-binding model of a one-dimensional semi-infinite chain, and we found that the calculated density of states agreed with the exact one. Surface states of the Newns-Anderson-Grimley model were also computed using the CAP, and the projected density of states on the adsorbed atom was successfully reproduced.
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Affiliation(s)
- Kosuke Imamura
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Tomokazu Yasuike
- Department of Liberal Arts, Faculty of Liberal Arts, The Open University of Japan, Chiba 261-8586, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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7
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Shi B, Zen A, Kapil V, Nagy PR, Grüneis A, Michaelides A. Many-Body Methods for Surface Chemistry Come of Age: Achieving Consensus with Experiments. J Am Chem Soc 2023; 145:25372-25381. [PMID: 37948071 PMCID: PMC10683001 DOI: 10.1021/jacs.3c09616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 11/12/2023]
Abstract
The adsorption energy of a molecule onto the surface of a material underpins a wide array of applications, spanning heterogeneous catalysis, gas storage, and many more. It is the key quantity where experimental measurements and theoretical calculations meet, with agreement being necessary for reliable predictions of chemical reaction rates and mechanisms. The prototypical molecule-surface system is CO adsorbed on MgO, but despite intense scrutiny from theory and experiment, there is still no consensus on its adsorption energy. In particular, the large cost of accurate many-body methods makes reaching converged theoretical estimates difficult, generating a wide range of values. In this work, we address this challenge, leveraging the latest advances in diffusion Monte Carlo (DMC) and coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] to obtain accurate predictions for CO on MgO. These reliable theoretical estimates allow us to evaluate the inconsistencies in published temperature-programed desorption experiments, revealing that they arise from variations in employed pre-exponential factors. Utilizing this insight, we derive new experimental estimates of the (electronic) adsorption energy with a (more) precise pre-exponential factor. As a culmination of all of this effort, we are able to reach a consensus between multiple theoretical calculations and multiple experiments for the first time. In addition, we show that our recently developed cluster-based CCSD(T) approach provides a low-cost route toward achieving accurate adsorption energies. This sets the stage for affordable and reliable theoretical predictions of chemical reactions on surfaces to guide the realization of new catalysts and gas storage materials.
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Affiliation(s)
- Benjamin
X. Shi
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
| | - Andrea Zen
- Dipartimento
di Fisica Ettore Pancini, Università
di Napoli Federico II, Monte S. Angelo, I-80126 Napoli, Italy
- Department
of Earth Sciences, University College London, Gower Street, WC1E 6BT London, U.K.
| | - Venkat Kapil
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
| | - Péter R. Nagy
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3, H-1111 Budapest, Hungary
- HUN-REN-BME
Quantum Chemistry Research Group, Müegyetem rkp. 3, H-1111 Budapest, Hungary
- MTA-BME
Lendület Quantum Chemistry Research Group, Müegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Andreas Grüneis
- Institute
for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10/136, 1040 Vienna, Austria
| | - Angelos Michaelides
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
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8
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Mysovsky AS, Bogdanov AI. Seamless Multilayer─A Novel Total Energy Partition Scheme for Embedded and Hybrid Calculations. J Chem Theory Comput 2023. [PMID: 37973151 DOI: 10.1021/acs.jctc.3c00666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
In this paper, we provide general formulation of a multilayer approach, covering both additive and subtractive quantum mechanics/molecular mechanics (QM/MM) as special cases. After that, we suggest a novel definition of QM/MM total energy based on the consideration of a system divided into three layers. In a simplified form, it is E = E Q M ( 1 + 2 ) - E Q M ( 2 ) + E M M ( 2 + 3 ) , where layers 1, 2, and 3 represent inner QM, outer QM, and classical MM regions, respectively. The novel formulation is also not limited by only QM/MM combination of methods─in fact, any computational methods can be combined in a hybrid calculation. In this paper, we call the new approach seamless multilayer. Test calculations performed for silica and boric oxide show that the new approach requires no QM/MM interface parameterization as well as no or very simple correction terms for boundary atoms. This can greatly facilitate QM/MM studies of covalent inorganic solids. However, test calculations of α-Al2O3 show that for ionic compounds, the new method requires some additional development.
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Affiliation(s)
- Andrey S Mysovsky
- A.P. Vinogradov Institute of Geochemistry SB RAS, 1a Favorsky Street, 664033 Irkutsk, Russia
- Institute of Quantum Physics, Irkutsk National Research Technical University, 83 Lermontov Street, 664074 Irkutsk, Russia
| | - Alexander I Bogdanov
- A.P. Vinogradov Institute of Geochemistry SB RAS, 1a Favorsky Street, 664033 Irkutsk, Russia
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Iaia EP, Soyemi A, Szilvási T, Harris JW. Zeolite encapsulated organometallic complexes as model catalysts. Dalton Trans 2023; 52:16103-16112. [PMID: 37812079 DOI: 10.1039/d3dt02126b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Heterogeneities in the structure of active centers in metal-containing porous materials are unavoidable and complicate the description of chemical events occurring along reaction coordinates at the atomic level. Metal containing zeolites include sites of varied local coordination and secondary confining environments, requiring careful titration protocols to quantify the predominant active sites. Hybrid organometallic-zeolite catalysts are useful well-defined platform materials for spectroscopic, kinetic, and computational studies of heterogeneous catalysis that avoid the complications of conventional metal-containing porous materials. Such materials have been synthesized and studied previously, but catalytic applications were mostly limited to liquid-phase oxidation and electrochemical reactions. The hydrothermal stability, time-on-stream stability, and utility of these materials in gas-phase oxidation reactions are under-studied. The potential applications for single-site heterogeneous catalysts in fundamental research are abundant and motivate future synthetic, spectroscopic, kinetic, and computational studies.
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Affiliation(s)
- Ethan P Iaia
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL, 35487, USA.
| | - Ademola Soyemi
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL, 35487, USA.
| | - Tibor Szilvási
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL, 35487, USA.
| | - James W Harris
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL, 35487, USA.
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10
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Plett C, Katbashev A, Ehlert S, Grimme S, Bursch M. ONIOM meets xtb: efficient, accurate, and robust multi-layer simulations across the periodic table. Phys Chem Chem Phys 2023. [PMID: 37378957 DOI: 10.1039/d3cp02178e] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
The computational treatment of large molecular structures is of increasing interest in fields of modern chemistry. Accordingly, efficient quantum chemical approaches are needed to perform sophisticated investigations on such systems. This engaged the development of the well-established "Our own N-layered integrated molecular orbital and molecular mechanics" (ONIOM) multi-layer scheme [L. W. Chung et al., Chem. Rev., 2015, 115, 5678-5796]. In this work, we present the specific implementation of the ONIOM scheme into the xtb semi-empirical extended tight-binding program package and its application to challenging transition-metal complexes. The efficient and broadly applicable GFNn-xTB and -FF methods are applied in the ONIOM framework to elucidate reaction energies, geometry optimizations, and explicit solvation effects for metal-organic systems with up to several hundreds of atoms. It is shown that an ONIOM-based combination of density functional theory, semi-empirical, and force-field methods can be used to drastically reduce the computational costs and thus enable the investigation of huge systems at almost no significant loss in accuracy.
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Affiliation(s)
- Christoph Plett
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Abylay Katbashev
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Sebastian Ehlert
- Microsoft Research AI4Science, Evert van de Beekstraat 254, 1118 CZ Schiphol, The Netherlands
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Markus Bursch
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
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