1
|
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.
Collapse
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
| |
Collapse
|
2
|
Ditte M, Barborini M, Medrano Sandonas L, Tkatchenko A. Molecules in Environments: Toward Systematic Quantum Embedding of Electrons and Drude Oscillators. PHYSICAL REVIEW LETTERS 2023; 131:228001. [PMID: 38101380 DOI: 10.1103/physrevlett.131.228001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/26/2023] [Accepted: 10/20/2023] [Indexed: 12/17/2023]
Abstract
We develop a quantum embedding method that enables accurate and efficient treatment of interactions between molecules and an environment, while explicitly including many-body correlations. The molecule is composed of classical nuclei and quantum electrons, whereas the environment is modeled via charged quantum harmonic oscillators. We construct a general Hamiltonian and introduce a variational Ansatz for the correlated ground state of the fully interacting molecule-environment system. This wave function is optimized via the variational Monte Carlo method and the ground state energy is subsequently estimated through the diffusion Monte Carlo method. The proposed scheme allows an explicit many-body treatment of electrostatic, polarization, and dispersion interactions between the molecule and the environment. We study solvation energies and excitation energies of benzene derivatives, obtaining excellent agreement with explicit ab initio calculations and experiments.
Collapse
Affiliation(s)
- Matej Ditte
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Matteo Barborini
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Leonardo Medrano Sandonas
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| |
Collapse
|
3
|
Tripathy V, Raghavachari K. EE-ONIOM-CT Method to Efficiently Account for the Missing Interactions in ONIOM: Energies and Analytic Gradients. J Chem Theory Comput 2023; 19:5791-5805. [PMID: 37581381 DOI: 10.1021/acs.jctc.3c00497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Hybrid methods such as ONIOM (QM:QM) are widely used for the study of local processes in large systems. However, the intrinsic need for system partitioning often leads to a less-than-desirable performance for some important chemical processes. This is due to the missing interactions in the chemically important model region (i.e., active site) of the high-level theory. The missing interactions can be categorized into two classes, viz. charge transfer (i.e., charge redistribution) and long-range electrostatic interactions. Our group presented two entirely different methods to treat these deficiencies individually. ONIOM-CT and ONIOM-EE methods have been demonstrated to improve the performance of ONIOM by incorporating charge transfer and missing electrostatic interactions, respectively. In general, the inclusion of the missing interactions separately in two different calculations may not be sufficient to reach a high accuracy. Thus, it is highly desirable to develop a method to correct both deficiencies simultaneously. In this work, we aim to connect the methods ONIOM-CT and ONIOM-EE for a more comprehensive treatment. A "stepwise" model was found to be necessary for a robust performance. This model employs a stepwise procedure by first satisfying the ONIOM-CT condition for charge balance before accounting for the electrostatic interactions from the rest of the system perturbatively. This has the advantage of easy interpretation due to the clear separation of the two effects. We demonstrate the performance of our method using embedding charges determined from a Mulliken population analysis. An efficient analytic gradient expression for this method is derived and implemented by requiring three sets of z-vector self-consistent equations. The performance of our method is assessed against full system calculations in high-level theory for a set of three proton transfer reactions representing different degrees of electrostatic embedding.
Collapse
Affiliation(s)
- Vikrant Tripathy
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| |
Collapse
|
4
|
Bramley GA, Beynon OT, Stishenko PV, Logsdail AJ. The application of QM/MM simulations in heterogeneous catalysis. Phys Chem Chem Phys 2023; 25:6562-6585. [PMID: 36810655 DOI: 10.1039/d2cp04537k] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The QM/MM simulation method is provenly efficient for the simulation of biological systems, where an interplay of extensive environment and delicate local interactions drives a process of interest through a funnel on a complex energy landscape. Recent advances in quantum chemistry and force-field methods present opportunities for the adoption of QM/MM to simulate heterogeneous catalytic processes, and their related systems, where similar intricacies exist on the energy landscape. Herein, the fundamental theoretical considerations for performing QM/MM simulations, and the practical considerations for setting up QM/MM simulations of catalytic systems, are introduced; then, areas of heterogeneous catalysis are explored where QM/MM methods have been most fruitfully applied. The discussion includes simulations performed for adsorption processes in solvent at metallic interfaces, reaction mechanisms within zeolitic systems, nanoparticles, and defect chemistry within ionic solids. We conclude with a perspective on the current state of the field and areas where future opportunities for development and application exist.
Collapse
Affiliation(s)
- Gabriel Adrian Bramley
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Park Place, CF10 3AT, UK.
| | - Owain Tomos Beynon
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Park Place, CF10 3AT, UK.
| | | | - Andrew James Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Park Place, CF10 3AT, UK.
| |
Collapse
|
5
|
Tripathy V, Mayhall NJ, Raghavachari K. ONIOM Method with Charge Transfer Corrections (ONIOM-CT): Analytic Gradients and Benchmarking. J Chem Theory Comput 2022; 18:6052-6064. [PMID: 36154125 DOI: 10.1021/acs.jctc.2c00584] [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
Hybrid methods such as ONIOM that treat different regions of a large molecule using different methods are widely used to investigate chemical reactions in a variety of materials and biological systems. However, there are inherent sources of significant errors due to the standard treatment of the boundary between the regions using hydrogen link atoms. In particular, an unbalanced charge distribution in the chemically important model region is a potential source of such problems. We have previously suggested ONIOM-CT (ONIOM with charge transfer corrections) which addresses this issue by applying a potential in the form of point charges to obtain a desired charge redistribution. The metric for charge redistribution relies on the type of population analysis used to obtain the charges. ONIOM-CT has been implemented using Mulliken and Löwdin population analyses and has been shown to improve computed reaction energies for illustrative chemical reactions. In this work, we derive and implement the analytic gradients for ONIOM-CT that requires solving two sets of coupled-perturbed self-consistent equations, one each for the model system and the full system. However, both are needed only at the low level of theory, allowing for an efficient formulation and implementation for both Mulliken and Löwdin population analyses. Benchmarking and illustrative geometry optimizations have been carried out for a previously studied set of reactions involving a single link atom between regions. Additionally, we have generalized our method for the treatment of model systems involving multiple link atoms to enable applications for a broader set of problems. The generalized methods are illustrated for both charge models. Furthermore, we have studied a set of three proton transfer reactions and demonstrate that significant improvement is achieved by ONIOM-CT over ONIOM using both Mulliken and Löwdin population analyses.
Collapse
Affiliation(s)
- Vikrant Tripathy
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Nicholas J Mayhall
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| |
Collapse
|
6
|
Shi BX, Kapil V, Zen A, Chen J, Alavi A, Michaelides A. General embedded cluster protocol for accurate modeling of oxygen vacancies in metal-oxides. J Chem Phys 2022; 156:124704. [DOI: 10.1063/5.0087031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The O vacancy (Ov) formation energy, EOv, is an important property of a metal-oxide, governing its performance in applications such as fuel cells or heterogeneous catalysis. These defects are routinely studied with density functional theory (DFT). However, it is well-recognized that standard DFT formulations (e.g., the generalized gradient approximation) are insufficient for modeling the Ov, requiring higher levels of theory. The embedded cluster method offers a promising approach to compute EOv accurately, giving access to all electronic structure methods. Central to this approach is the construction of quantum(-mechanically treated) clusters placed within suitable embedding environments. Unfortunately, current approaches to constructing the quantum clusters either require large system sizes, preventing application of high-level methods, or require significant manual input, preventing investigations of multiple systems simultaneously. In this work, we present a systematic and general quantum cluster design protocol that can determine small converged quantum clusters for studying the Ov in metal-oxides with accurate methods, such as local coupled cluster with single, double, and perturbative triple excitations. We apply this protocol to study the Ov in the bulk and surface planes of rutile TiO2 and rock salt MgO, producing the first accurate and well-converged determinations of EOv with this method. These reference values are used to benchmark exchange–correlation functionals in DFT, and we find that all the studied functionals underestimate EOv, with the average error decreasing along the rungs of Jacob’s ladder. This protocol is automatable for high-throughput calculations and can be generalized to study other point defects or adsorbates.
Collapse
Affiliation(s)
- Benjamin X. Shi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Venkat Kapil
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Churchill College, University of Cambridge, Storey’s Way, Cambridge CB3 0DS, United Kingdom
| | - 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, London WC1E 6BT, United Kingdom
| | - Ji Chen
- School of Physics, Peking University, Beijing 100871, China
| | - Ali Alavi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Angelos Michaelides
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| |
Collapse
|
7
|
Jones LO, Mosquera MA, Schatz GC, Ratner MA. Embedding Methods for Quantum Chemistry: Applications from Materials to Life Sciences. J Am Chem Soc 2020; 142:3281-3295. [PMID: 31986877 DOI: 10.1021/jacs.9b10780] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Quantum mechanical embedding methods hold the promise to transform not just the way calculations are performed, but to significantly reduce computational costs and improve scaling for macro-molecular systems containing hundreds if not thousands of atoms. The field of embedding has grown increasingly broad with many approaches of different intersecting flavors. In this perspective, we lay out the methods into two streams: QM:MM and QM:QM, showcasing the advantages and disadvantages of both. We provide a review of the literature, the underpinning theories including our contributions, and we highlight current applications with select examples spanning both materials and life sciences. We conclude with prospects and future outlook on embedding, and our view on the use of universal test case scenarios for cross-comparisons of the many available (and future) embedding theories.
Collapse
Affiliation(s)
- Leighton O Jones
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Martín A Mosquera
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - George C Schatz
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Mark A Ratner
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| |
Collapse
|
8
|
Vummaleti SVC, Kuriakose N, Dinda S, Wu Y, Genest A, Rösch N. C–C coupling at a zeolite-supported Rh(i) complex. DFT search for the mechanism. Catal Sci Technol 2019. [DOI: 10.1039/c9cy00617f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DFT modelling suggests a metallacycle mechanism for the dimerization of ethene over a faujasite-supported Rh(i) complex, rationalizing the experimental selectivity.
Collapse
Affiliation(s)
- Sai V. C. Vummaleti
- Institute of High Performance Computing
- Agency for Science, Technology and Research
- 138632 Singapore
| | - Nishamol Kuriakose
- Institute of High Performance Computing
- Agency for Science, Technology and Research
- 138632 Singapore
| | - Shrabani Dinda
- Institute of High Performance Computing
- Agency for Science, Technology and Research
- 138632 Singapore
| | - Yin Wu
- Institute of High Performance Computing
- Agency for Science, Technology and Research
- 138632 Singapore
- Department Chemie and Catalysis Research Center
- Technische Universität München
| | - Alexander Genest
- Institute of High Performance Computing
- Agency for Science, Technology and Research
- 138632 Singapore
| | - Notker Rösch
- Institute of High Performance Computing
- Agency for Science, Technology and Research
- 138632 Singapore
- Department Chemie and Catalysis Research Center
- Technische Universität München
| |
Collapse
|
9
|
Vummaleti SVC, Genest A, Kuriakose N, Rösch N. Ethene Dimerization and Hydrogenation over a Zeolite-Supported Rh(I)-Carbonyl Complex: Mechanistic Insights from DFT Modeling. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02573] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sai V. C. Vummaleti
- Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Singapore
| | - Alexander Genest
- Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Singapore
| | - Nishamol Kuriakose
- Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Singapore
| | - Notker Rösch
- Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Singapore
- Department Chemie and Catalysis Research Center, Technische Universität München, 85747 Garching, Germany
| |
Collapse
|
10
|
Sahoo SK, Nair NN. Interfacing the Core-Shell or the Drude Polarizable Force Field With Car-Parrinello Molecular Dynamics for QM/MM Simulations. Front Chem 2018; 6:275. [PMID: 30042939 PMCID: PMC6048201 DOI: 10.3389/fchem.2018.00275] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/18/2018] [Indexed: 11/13/2022] Open
Abstract
We report a quantum mechanics/polarizable–molecular mechanics (QM/p–MM) potential based molecular dynamics (MD) technique where the core–shell (or the Drude) type polarizable MM force field is interfaced with the plane-wave density functional theory based QM force field which allows Car–Parrinello MD for the QM subsystem. In the QM/p-MM Lagrangian proposed here, the shell (or the Drude) MM variables are treated as extended degrees of freedom along with the Kohn–Sham (KS) orbitals describing the QM wavefunction. The shell and the KS orbital degrees of freedom are then adiabatically decoupled from the nuclear degrees of freedom. In this respect, we also present here the Nosé–Hoover Chain thermostat implementation for the dynamical subsystems. Our approach is then used to investigate the effect of MM polarization on the QM/MM results. Especially, the consequence of MM polarization on reaction free energy barriers, defect formation energy, and structural and dynamical properties are investigated. A low point charge polarizable potential (p–MZHB) for pure siliceous systems is also reported here.
Collapse
Affiliation(s)
- Sudhir K Sahoo
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| |
Collapse
|
11
|
Chulhai DV, Goodpaster JD. Projection-Based Correlated Wave Function in Density Functional Theory Embedding for Periodic Systems. J Chem Theory Comput 2018; 14:1928-1942. [DOI: 10.1021/acs.jctc.7b01154] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Dhabih V. Chulhai
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Jason D. Goodpaster
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
12
|
O'Malley AJ, Logsdail AJ, Sokol AA, Catlow CRA. Modelling metal centres, acid sites and reaction mechanisms in microporous catalysts. Faraday Discuss 2018; 188:235-55. [PMID: 27136967 DOI: 10.1039/c6fd00010j] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We discuss the role of QM/MM (embedded cluster) computational techniques in catalytic science, in particular their application to microporous catalysis. We describe the methodologies employed and illustrate their utility by briefly summarising work on metal centres in zeolites. We then report a detailed investigation into the behaviour of methanol at acidic sites in zeolites H-ZSM-5 and H-Y in the context of the methanol-to-hydrocarbons/olefins process. Studying key initial steps of the reaction (the adsorption and subsequent methoxylation), we probe the effect of framework topology and Brønsted acid site location on the energetics of these initial processes. We find that although methoxylation is endothermic with respect to the adsorbed system (by 17-56 kJ mol(-1) depending on the location), there are intriguing correlations between the adsorption/reaction energies and the geometries of the adsorbed species, of particular significance being the coordination of methyl hydrogens. These observations emphasise the importance of adsorbate coordination with the framework in zeolite catalysed conversions, and how this may vary with framework topology and site location, particularly suited to investigation by QM/MM techniques.
Collapse
Affiliation(s)
- Alexander J O'Malley
- Department of Chemistry, University College London, 20 Gordon St., London WC1 HOAJ, UK and UK Catalysis Hub, Research Complex at Harwell, Science and Technology Facilities Council Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Oxon OX11 0QX, UK
| | - A J Logsdail
- Department of Chemistry, University College London, 20 Gordon St., London WC1 HOAJ, UK and Cardiff Catalysis Institute, School of Chemistry, Cardiff University, CF10 3AT, UK
| | - A A Sokol
- Department of Chemistry, University College London, 20 Gordon St., London WC1 HOAJ, UK
| | - C R A Catlow
- Department of Chemistry, University College London, 20 Gordon St., London WC1 HOAJ, UK and Cardiff Catalysis Institute, School of Chemistry, Cardiff University, CF10 3AT, UK and UK Catalysis Hub, Research Complex at Harwell, Science and Technology Facilities Council Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Oxon OX11 0QX, UK
| |
Collapse
|
13
|
Ivanova-Shor EA, Shor AM, Laletina SS, Deka RC, Nasluzov VA. Modeling of heterogeneous catalysts based on silica and zeolites by the hybrid quantum chemical embedded cluster method. Russ Chem Bull 2017. [DOI: 10.1007/s11172-017-1808-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
14
|
Sahoo SK, Nair NN. CPMD/GULP QM/MM interface for modeling periodic solids: Implementation and its application in the study of Y-zeolite supported Rhn clusters. J Comput Chem 2016; 37:1657-67. [PMID: 27092962 DOI: 10.1002/jcc.24379] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 02/29/2016] [Accepted: 03/14/2016] [Indexed: 11/11/2022]
Abstract
We report here the development of hybrid quantum mechanics/molecular mechanics (QM/MM) interface between the plane-wave density functional theory based CPMD code and the empirical force-field based GULP code for modeling periodic solids and surfaces. The hybrid QM/MM interface is based on the electrostatic coupling between QM and MM regions. The interface is designed for carrying out full relaxation of all the QM and MM atoms during geometry optimizations and molecular dynamics simulations, including the boundary atoms. Both Born-Oppenheimer and Car-Parrinello molecular dynamics schemes are enabled for the QM part during the QM/MM calculations. This interface has the advantage of parallelization of both the programs such that the QM and MM force evaluations can be carried out in parallel to model large systems. The interface program is first validated for total energy conservation and parallel scaling performance is benchmarked. Oxygen vacancy in α-cristobalite is then studied in detail and the results are compared with a fully QM calculation and experimental data. Subsequently, we use our implementation to investigate the structure of rhodium cluster (Rhn ; n = 2 to 6) formed from Rh(C2 H4 )2 complex adsorbed within a cavity of Y-zeolite in a reducible atmosphere of H2 gas. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Sudhir K Sahoo
- Department of Chemistry, Indian Institute of Technology, Kanpur, 208016, India
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology, Kanpur, 208016, India
| |
Collapse
|
15
|
Nasluzov VA, Parker SM, Genest A, Shor AM, Ivanova-Shor EA, Rösch N. Trinuclear tantalum clusters grafted to hydroxylated silica surfaces: A density-functional embedded-cluster study. KINETICS AND CATALYSIS 2015. [DOI: 10.1134/s0023158415050134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
16
|
Sahoo SK, Nair NN. A potential with low point charges for pure siliceous zeolites. J Comput Chem 2015; 36:1562-7. [PMID: 26073460 DOI: 10.1002/jcc.23968] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 05/19/2015] [Accepted: 05/25/2015] [Indexed: 12/11/2022]
Abstract
A modified CHARMM force-field (ZHB potential) with low point charges for silica was previously proposed by Zimmerman et al. (J. Chem. Theory Comput. 2011, 7, 1695). The ZHB potential is advantageous for quantum mechanics/molecular mechanics simulations as it minimizes the electron spill-out problems. In the same spirit, here we propose a modified ZHB potential (MZHB) by reformulating its bonding potential, while retaining the nonbonding potential as in the ZHB force-field. We show that several structural and dynamic properties of silica, like the IR spectrum, distribution functions, mechanical properties, and negative thermal expansion computed using the MZHB potential agree well with experimental data. Further, transferability of MZHB is also tested for reproducing the crystallographic structures of several polymorphs of silica. © 2015 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Sudhir K Sahoo
- Department of Chemistry, Indian Institute of Technology, Kanpur, 208016, India
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology, Kanpur, 208016, India
| |
Collapse
|
17
|
Kessler J, Bouř P. Transfer of Frequency-Dependent Polarizabilities: A Tool To Simulate Absorption and Circular Dichroism Molecular Spectra. J Chem Theory Comput 2015; 11:2210-20. [DOI: 10.1021/acs.jctc.5b00136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jiří Kessler
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, 166
10 Prague, Czech Republic
- Department
of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 40 Prague, Czech Republic
| | - Petr Bouř
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, 166
10 Prague, Czech Republic
| |
Collapse
|
18
|
Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 743] [Impact Index Per Article: 82.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| |
Collapse
|
19
|
Raghavachari K, Saha A. Accurate Composite and Fragment-Based Quantum Chemical Models for Large Molecules. Chem Rev 2015; 115:5643-77. [PMID: 25849163 DOI: 10.1021/cr500606e] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Krishnan Raghavachari
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Arjun Saha
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| |
Collapse
|
20
|
Chiu CC, Vayssilov GN, Genest A, Borgna A, Rösch N. Predicting adsorption enthalpies on silicalite and HZSM-5: A benchmark study on DFT strategies addressing dispersion interactions. J Comput Chem 2014; 35:809-19. [PMID: 24550154 DOI: 10.1002/jcc.23558] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 12/07/2013] [Accepted: 01/09/2014] [Indexed: 11/11/2022]
Abstract
We evaluated the accuracy of periodic density functional calculations for adsorption enthalpies of water, alkanes, and alcohols in silicalite and HZSM-5 zeolites using a gradient-corrected density functional with empirical dispersion corrections (PBE-D) as well as a nonlocal correlation functional (vdW-DF2). Results of both approaches agree in acceptable fashion with experimental adsorption energies of alcohols in silicalite, but the adsorption energies for n-alkanes in both zeolite models are overestimated, by 21-46 kJ mol(-1). For PBE-D calculations, the adsorption of alkanes is exclusively determined by the empirical dispersion term, while the generalized gradient approximation-DFT part is purely repulsive, preventing the molecule to come too close to the zeolite walls. The vdW-DF2 results are comparable to those of PBE-D calculations, but the latter values are slightly closer to the experiment in most cases. Thus, both computational approaches are unable to reproduce available experimental adsorption energies of alkanes in silicalite and HZSM-5 zeolite with chemical accuracy.
Collapse
Affiliation(s)
- Cheng-chau Chiu
- Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Singapore.,Department Chemie and Catalysis Research Center, Technische Universität München, 85747, Garching, Germany.,Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, 1 Pesek Road, Jurong Island, Singapore, 627833, Singapore
| | - Georgi N Vayssilov
- Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Singapore.,Faculty of Chemistry and Pharmacy, University of Sofia, Blvd. J. Baucher 1, 1126, Sofia, Bulgaria
| | - Alexander Genest
- Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Singapore
| | - Armando Borgna
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, 1 Pesek Road, Jurong Island, Singapore, 627833, Singapore
| | - Notker Rösch
- Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, #16-16 Connexis, Singapore, 138632, Singapore.,Department Chemie and Catalysis Research Center, Technische Universität München, 85747, Garching, Germany
| |
Collapse
|
21
|
Isegawa M, Wang B, Truhlar DG. Electrostatically Embedded Molecular Tailoring Approach and Validation for Peptides. J Chem Theory Comput 2013; 9:1381-93. [DOI: 10.1021/ct300845q] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Miho Isegawa
- Department of Chemistry, Chemical Theory Center, and
Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
55455-0431, United States
| | - Bo Wang
- Department of Chemistry, Chemical Theory Center, and
Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
55455-0431, United States
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and
Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
55455-0431, United States
| |
Collapse
|
22
|
Sousa C, Tosoni S, Illas F. Theoretical Approaches to Excited-State-Related Phenomena in Oxide Surfaces. Chem Rev 2012. [DOI: 10.1021/cr300228z] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Carmen Sousa
- Departament de Química
Física and Institut de Química Teòrica i Computacional
(IQTCUB), Universitat de Barcelona, C/Martí
i Franquès 1, 08028 Barcelona, Spain
| | - Sergio Tosoni
- Departament de Química
Física and Institut de Química Teòrica i Computacional
(IQTCUB), Universitat de Barcelona, C/Martí
i Franquès 1, 08028 Barcelona, Spain
- Departamento de Química, Universidad de Las Palmas de Gran Canaria, Campus Universitario
de Tafira, 35017 Las Palmas de Gran Canaria, Spain
| | - Francesc Illas
- Departament de Química
Física and Institut de Química Teòrica i Computacional
(IQTCUB), Universitat de Barcelona, C/Martí
i Franquès 1, 08028 Barcelona, Spain
| |
Collapse
|
23
|
Guo W, Wu A, Zhang IY, Xu X. XO: An extended ONIOM method for accurate and efficient modeling of large systems. J Comput Chem 2012; 33:2142-60. [DOI: 10.1002/jcc.23051] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 06/04/2012] [Accepted: 06/05/2012] [Indexed: 11/10/2022]
|
24
|
Severo Pereira Gomes A, Jacob CR. Quantum-chemical embedding methods for treating local electronic excitations in complex chemical systems. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2pc90007f] [Citation(s) in RCA: 165] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
25
|
Vayssilov GN, Petrova GP, Shor EAI, Nasluzov VA, Shor AM, Petkov PS, Rösch N. Reverse hydrogen spillover on and hydrogenation of supported metal clusters: insights from computational model studies. Phys Chem Chem Phys 2012; 14:5879-90. [DOI: 10.1039/c2cp23648f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
26
|
Walsh A, Catlow CRA, Miskufova M, Sokol AA. Electron and hole stability in GaN and ZnO. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2011; 23:334217. [PMID: 21813955 DOI: 10.1088/0953-8984/23/33/334217] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We assess the thermodynamic doping limits of GaN and ZnO on the basis of point defect calculations performed using the embedded cluster approach and employing a hybrid non-local density functional for the quantum mechanical region. Within this approach we have calculated a staggered (type-II) valence band alignment between the two materials, with the N 2p states contributing to the lower ionization potential of GaN. With respect to the stability of free electron and hole carriers, redox reactions resulting in charge compensation by ionic defects are found to be largely endothermic (unfavourable) for electrons and exothermic (favourable) for holes, which is consistent with the efficacy of electron conduction in these materials. Approaches for overcoming these fundamental thermodynamic limits are discussed.
Collapse
Affiliation(s)
- Aron Walsh
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
| | | | | | | |
Collapse
|
27
|
Zimmerman PM, Head-Gordon M, Bell AT. Selection and Validation of Charge and Lennard-Jones Parameters for QM/MM Simulations of Hydrocarbon Interactions with Zeolites. J Chem Theory Comput 2011; 7:1695-703. [DOI: 10.1021/ct2001655] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Paul M. Zimmerman
- Department of Chemistry, University of California, Berkeley, California 94720-1461, United States
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720-1461, United States
| | - Alexis T. Bell
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720-1462, United States
| |
Collapse
|
28
|
Nasluzov VA, Ivanova-Shor EA, Shor AM, Yudanov IV, Rösch N. Simulation of heterogeneous catalysts and catalytic processes using the density functional method. KINETICS AND CATALYSIS 2010. [DOI: 10.1134/s0023158410060091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
29
|
Abstract
Abstract
We overview quantum mechanical simulations that model the adsorption of actinide ions at solvated mineral surfaces. Pertinent examples illustrate the status of this emerging field of computational chemistry. In particular, we describe our own studies on uranyl adsorption on kaolinite. Already the few available results, from applications of density functional methods to cluster models or periodic slab models, show that such calculations are a useful complement to experimental investigations. Detailed information at the atomic level from accurate electronic structure calculations on well defined model systems helps to refine current interpretations of the chemical nature of uranyl adsorption species and to discover new features of these interface systems. Results from quantum mechanical simulations also provide a valuable reference for future experimental investigations.
Collapse
|
30
|
Aleksandrov HA, Vayssilov GN. Theoretical investigation of ethane dehydrogenation on cationic Zn species in ZSM-5 zeolites—The second Al center in vicinity of the cation is essential for the accomplishment of the complete catalytic cycle. Catal Today 2010. [DOI: 10.1016/j.cattod.2010.01.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
31
|
Affiliation(s)
- Peter V. Sushko
- Department of Physics and Astronomy and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom, WPI Advanced Institute for Materials Research, Tohoku University, Sendai 980-8577, Japan, and Department of Physics, St. Petersburg State University, St. Petersburg 198504, Russia
| | - Igor V. Abarenkov
- Department of Physics and Astronomy and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom, WPI Advanced Institute for Materials Research, Tohoku University, Sendai 980-8577, Japan, and Department of Physics, St. Petersburg State University, St. Petersburg 198504, Russia
| |
Collapse
|
32
|
Wang B, Truhlar DG. Combined Quantum Mechanical and Molecular Mechanical Methods for Calculating Potential Energy Surfaces: Tuned and Balanced Redistributed-Charge Algorithm. J Chem Theory Comput 2010; 6:359-69. [DOI: 10.1021/ct900366m] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bo Wang
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street South East, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street South East, Minneapolis, Minnesota 55455-0431
| |
Collapse
|
33
|
Shor AM, Shor EAI, Laletina S, Nasluzov VA, Vayssilov GN, Rösch N. Effect of the size of the quantum region in a hybrid embedded-cluster scheme for zeolite systems. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2009.07.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
34
|
Huang P, Carter EA. Advances in correlated electronic structure methods for solids, surfaces, and nanostructures. Annu Rev Phys Chem 2008; 59:261-90. [PMID: 18031211 DOI: 10.1146/annurev.physchem.59.032607.093528] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Calculations of the electronic structure of solids began decades ago, but only recently have solid-state quantum techniques become sufficiently reliable that their application is nearly as routine as quantum chemistry is for molecules. We aim to introduce chemists to the pros and cons of first-principles methods that can provide atomic-scale insight into the properties and chemistry of bulk materials, interfaces, and nanostructures. The techniques we review include the ubiquitous density functional theory (DFT), which is often sufficient, especially for metals; extensions such as DFT + U and hybrid DFT, which incorporate exact exchange to rid DFT of its spurious self-interactions (critical for some semiconductors and strongly correlated materials); many-body Green's function (GW and Bethe-Salpeter) methods for excited states; quantum Monte Carlo, in principle an exact theory but for which forces (hence structure optimization and dynamics) are problematic; and embedding theories that locally refine the quantum treatment to improve accuracy.
Collapse
Affiliation(s)
- Patrick Huang
- Department of Mechanical and Aerospace Engineering and Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544-5263, USA
| | | |
Collapse
|
35
|
Shor AM, Shor EAI, Nasluzov VA, Vayssilov GN, Rösch N. First Hybrid Embedding Scheme for Polar Covalent Materials Using an Extended Border Region To Minimize Boundary Effects on the Quantum Region. J Chem Theory Comput 2007; 3:2290-300. [DOI: 10.1021/ct700159k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexei M. Shor
- Institute of Chemistry and Chemical Technology, Russian Academy of Sciences, 660049 Krasnoyarsk, Russian Federation, Faculty of Chemistry, University of Sofia, 1126 Sofia, Bulgaria, and Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Elena A. Ivanova Shor
- Institute of Chemistry and Chemical Technology, Russian Academy of Sciences, 660049 Krasnoyarsk, Russian Federation, Faculty of Chemistry, University of Sofia, 1126 Sofia, Bulgaria, and Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Vladimir A. Nasluzov
- Institute of Chemistry and Chemical Technology, Russian Academy of Sciences, 660049 Krasnoyarsk, Russian Federation, Faculty of Chemistry, University of Sofia, 1126 Sofia, Bulgaria, and Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Georgi N. Vayssilov
- Institute of Chemistry and Chemical Technology, Russian Academy of Sciences, 660049 Krasnoyarsk, Russian Federation, Faculty of Chemistry, University of Sofia, 1126 Sofia, Bulgaria, and Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Notker Rösch
- Institute of Chemistry and Chemical Technology, Russian Academy of Sciences, 660049 Krasnoyarsk, Russian Federation, Faculty of Chemistry, University of Sofia, 1126 Sofia, Bulgaria, and Department Chemie, Technische Universität München, 85747 Garching, Germany
| |
Collapse
|
36
|
Nachtigall P, Sauer J. Applications of Quantum Chemical Methods in Zeolite Science. STUDIES IN SURFACE SCIENCE AND CATALYSIS 2007. [DOI: 10.1016/s0167-2991(07)80808-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
37
|
Otero Areán C, Nachtigallová D, Nachtigall P, Garrone E, Rodríguez Delgado M. Thermodynamics of reversible gas adsorption on alkali-metal exchanged zeolites—the interplay of infrared spectroscopy and theoretical calculations. Phys Chem Chem Phys 2007; 9:1421-37. [PMID: 17356750 DOI: 10.1039/b615535a] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Detailed understanding of weak solid-gas interactions giving rise to reversible gas adsorption on zeolites and related materials is relevant to both, fundamental studies on gas adsorption and potential improvement on a number of (adsorption based) technological processes. Combination of variable-temperature infrared spectroscopy with theoretical calculations constitutes a fruitful approach towards both of these aims. Such an approach is demonstrated here (mainly) by reviewing recent studies on hydrogen and carbon monoxide adsorption (at a low temperature) on alkali-metal exchanged ferrierite. However, the methodology discussed, which involves the interplay of experimental measurements and theoretical calculations at the periodic DFT level, should be equally valid for many other gas-solid systems. Specific aspects considered are the identification of gas adsorption complexes and thermodynamic studies related to standard adsorption enthalpy and entropy.
Collapse
Affiliation(s)
- C Otero Areán
- Departamento de Química, Universidad de las Islas Baleares, E-07122 Palma de Mallorca, Spain.
| | | | | | | | | |
Collapse
|
38
|
Cinquini F, Valentin CD, Finazzi E, Giordano L, Pacchioni G. Theory of oxides surfaces, interfaces and supported nano-clusters. Theor Chem Acc 2006. [DOI: 10.1007/s00214-006-0204-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
39
|
Neyman KM, Inntam C, Moskaleva LV, Rösch N. Density Functional Embedded Cluster Study of Cu4, Ag4and Au4Species Interacting with Oxygen Vacancies on the MgO(001) Surface. Chemistry 2006; 13:277-86. [PMID: 16969882 DOI: 10.1002/chem.200600545] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cu(4), Ag(4), and Au(4) species adsorbed on an MgO(001) surface that exhibits neutral (F(s)) and charged (F(s) (+)) oxygen vacancies have been studied using a density functional approach and advanced embedding models. The gas-phase rhombic-planar structure of the coinage metal tetramers is only moderately affected by adsorption. In the most stable surface configuration, the plane of the tetramers is oriented perpendicular to the MgO(001) surface; one metal atom is attached to an oxygen vacancy and another one is bound to a nearby surface oxygen anion. A very similar structural motif was recently found on defect-free MgO(001), where two O(2-) ions serve as adsorption sites. Following the trend of the interactions with the regular MgO(001) surface, Au(4) and Cu(4) bind substantially stronger to F(s) and F(s) (+) sites than Ag(4). This stronger adsorption interaction at oxygen vacancies, in particular at F(s), is partly due to a notable accumulation of electron density on the adsorbates. We also examined the propensity of small supported metal species to aggregate to adsorbed di-, tri- and tetramers. Furthermore, we demonstrated that core-level ionization potentials offer the possibility for detecting experimentally supported metal tetramers and characterizing them structurally with the help of calculated data.
Collapse
Affiliation(s)
- Konstantin M Neyman
- ICREA, 08010 Barcelona and Departament de Química Física, Universitat de Barcelona, 08028 Barcelona, Spain.
| | | | | | | |
Collapse
|
40
|
Abstract
The stability of rings in pure silica zeolite frameworks is investigated through a new method. The energetic terms influencing the stability of rings are evaluated through the short-range plus electrostatics corresponding to SiO bonds and OSiO and SiOSi angles. Several atomistic force fields have been evaluated, and a reparametrization of the Vessal-Leslie-Catlow force field has been chosen because of its physical meaning and good structural accuracy. The ring energetics are analyzed and discussed in terms of local strain in the framework and in terms of geometric variables. This methodology allows to differentiate between the strain of rings of a given size in different zeolite structures. In particular, it is found that double four rings (D4Rs) are not necessarily, as previously stated, a strained secondary building unit. The analyses of D4Rs in the topologies AST, BEC, and LTA allow the calculation of its stability in the different structures showing high energy in BEC and LTA and low energy in AST. Implications of these results on nucleation of zeolites are drawn regarding the facility with which D4Rs are inserted in different frameworks.
Collapse
Affiliation(s)
- German Sastre
- Instituto de Tecnologia Quimica UPV-CSIC, Universidad Politecnica de Valencia, Avda. Los Naranjos s/n, 46022 Valencia, Spain.
| | | |
Collapse
|
41
|
Deka RC, Nasluzov VA, Ivanova Shor EA, Shor AM, Vayssilov GN, Rösch N. Comparison of all sites for Ti substitution in zeolite TS-1 by an accurate embedded-cluster method. J Phys Chem B 2006; 109:24304-10. [PMID: 16375428 DOI: 10.1021/jp050056l] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We studied the preferential location of Ti centers in the framework of the Ti-containing MFI zeolite TS-1 using a hybrid DFT/MM embedding method developed recently. This "covalent elastic polarizable environment" (covEPE) cluster embedding allows a complete and self-consistent treatment of solid covalent systems such as zeolites. For the present study, we used a gradient-corrected density functional approach. The resulting structural features of both Si- and Ti-substituted forms of the zeolite framework fit well with available experimental information. The calculated substitution energy of Ti at the 12 crystallographically different tetrahedral sites of the MFI structure vary within 19 kJ/mol with T12 and T2 as most and least preferred sites, respectively. On the basis of these computational results and the preferential sites for Ti substitution reported from different experimental investigations, we concluded that the Ti distribution in the TS-1 framework is not governed by the thermodynamic stability of the pure material.
Collapse
Affiliation(s)
- Ramesh Ch Deka
- Department Chemie, Technische Universität München, 85747 Garching, Germany
| | | | | | | | | | | |
Collapse
|
42
|
Laino T, Mohamed F, Laio A, Parrinello M. An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations. J Chem Theory Comput 2006; 2:1370-8. [DOI: 10.1021/ct6001169] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Teodoro Laino
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56125 Pisa, Italy, and Computational Science, Department of Chemistry and Applied Biosciences, ETH Zürich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Fawzi Mohamed
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56125 Pisa, Italy, and Computational Science, Department of Chemistry and Applied Biosciences, ETH Zürich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Alessandro Laio
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56125 Pisa, Italy, and Computational Science, Department of Chemistry and Applied Biosciences, ETH Zürich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Michele Parrinello
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56125 Pisa, Italy, and Computational Science, Department of Chemistry and Applied Biosciences, ETH Zürich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| |
Collapse
|
43
|
Heterolytic dissociation and recombination of H2 over Zn,H-ZSM-5 zeolites—A density functional model study. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.molcata.2006.04.051] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
44
|
Zipoli F, Laino T, Laio A, Bernasconi M, Parrinello M. A QUICKSTEP-based quantum mechanics/molecular mechanics approach for silica. J Chem Phys 2006; 124:154707. [PMID: 16674251 DOI: 10.1063/1.2187485] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Quantum mechanics/molecular mechanics (QM/MM) approaches are currently used to describe several properties of silica-based systems, which are local in nature and require a quantum description of only a small number of atoms around the site of interest, e.g., local chemical reactivity or spectroscopic properties of point defects. We present a QM/MM scheme for silica suitable to be implemented in the general QM/MM framework recently developed for large scale molecular dynamics simulations, within the QUICKSTEP approach to the description of the quantum region. Our scheme has been validated by computing the structural and dynamical properties of an oxygen vacancy in alpha-quartz, a prototypical defect in silica. We have found that good convergence in the Si-Si bond length and formation energy is achieved by using a quantum cluster of only eight atoms in size. We check the suitability of the method for molecular dynamics and evaluate the Si-Si bond frequency from the velocity-velocity correlation function.
Collapse
Affiliation(s)
- Federico Zipoli
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, Via Cozzi 53, I-20125, Milano, Italy.
| | | | | | | | | |
Collapse
|
45
|
Del Vitto A, Pacchioni G, Lim KH, Rösch N, Antonietti JM, Michalski M, Heiz U, Jones H. Gold Atoms and Dimers on Amorphous SiO2: Calculation of Optical Properties and Cavity Ringdown Spectroscopy Measurements. J Phys Chem B 2005; 109:19876-84. [PMID: 16853570 DOI: 10.1021/jp054794l] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report on the optical absorption spectra of gold atoms and dimers deposited on amorphous silica in size-selected fashion. Experimental spectra were obtained by cavity ringdown spectroscopy. Issues on soft-landing, fragmentation, and thermal diffusion are discussed on the basis of the experimental results. In parallel, cluster and periodic supercell density functional theory (DFT) calculations were performed to model atoms and dimers trapped on various defect sites of amorphous silica. Optically allowed electronic transitions were calculated, and comparisons with the experimental spectra show that silicon dangling bonds [[triple bond]Si(.-)], nonbridging oxygen [[triple bond]Si-O(.-)], and the silanolate group [[triple bond]Si-O(-)] act as trapping centers for the gold particles. The results are not only important for understanding the chemical bonding of atoms and clusters on oxide surfaces, but they will also be of fundamental interest for photochemical studies of size-selected clusters on surfaces.
Collapse
Affiliation(s)
- Annalisa Del Vitto
- Dipartimento di Scienza dei Materiali, Universita di Milano-Bicocca, via R. Cozzi 53, I-20125 Milano, Italy
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Neyman KM, Inntam C, Matveev AV, Nasluzov VA, Rösch N. Single d-Metal Atoms on Fs and Fs+ Defects of MgO(001): A Theoretical Study across the Periodic Table. J Am Chem Soc 2005; 127:11652-60. [PMID: 16104741 DOI: 10.1021/ja052437i] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single d-metal atoms on oxygen defects F(s) and F(s+) of the MgO(001) surface were studied theoretically. We employed an accurate density functional method combined with cluster models, embedded in an elastic polarizable environment, and we applied two gradient-corrected exchange-correlation functionals. In this way, we quantified how 17 metal atoms from groups 6-11 of the periodic table (Cu, Ag, Au; Ni, Pd, Pt; Co, Rh, Ir; Fe, Ru, Os; Mn, Re; and Cr, Mo, W) interact with terrace sites of MgO. We found bonding with F(s) and F(s+) defects to be in general stronger than that with O2- sites, except for Mn-, Re-, and Fe/F(s) complexes. In M/F(s) systems, electron density is accumulated on the metal center in a notable fashion. The binding energy on both kinds of O defects increases from 3d- to 4d- to 5d-atoms of a given group, at variance with the binding energy trend established earlier for the M/O2- complexes, 4d < 3d < 5d. Regarding the evolution of the binding energy along a period, group 7 atoms are slightly destabilized compared to their group 6 congeners in both the F(s) and F(s+) complexes; for later transition elements, the binding energy increases gradually up to group 10 and finally decreases again in group 11, most strongly on the F(s) site. This trend is governed by the negative charge on the adsorbed atoms. We discuss implications for an experimental detection of metal atoms on oxide supports based on computed core-level energies.
Collapse
|
47
|
Ivanova Shor EA, Shor AM, Nasluzov VA, Vayssilov GN, Rösch N. Effects of the Aluminum Content of a Zeolite Framework: A DFT/MM Hybrid Approach Based on Cluster Models Embedded in an Elastic Polarizable Environment. J Chem Theory Comput 2005; 1:459-71. [DOI: 10.1021/ct049910n] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elena A. Ivanova Shor
- Institute of Chemistry and Chemical Technology, Russian Academy of Sciences, 660049 Krasnoyarsk, Russian Federation, Faculty of Chemistry, University of Sofia, 1126 Sofia, Bulgaria, and Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Alexei M. Shor
- Institute of Chemistry and Chemical Technology, Russian Academy of Sciences, 660049 Krasnoyarsk, Russian Federation, Faculty of Chemistry, University of Sofia, 1126 Sofia, Bulgaria, and Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Vladimir A. Nasluzov
- Institute of Chemistry and Chemical Technology, Russian Academy of Sciences, 660049 Krasnoyarsk, Russian Federation, Faculty of Chemistry, University of Sofia, 1126 Sofia, Bulgaria, and Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Georgi N. Vayssilov
- Institute of Chemistry and Chemical Technology, Russian Academy of Sciences, 660049 Krasnoyarsk, Russian Federation, Faculty of Chemistry, University of Sofia, 1126 Sofia, Bulgaria, and Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Notker Rösch
- Institute of Chemistry and Chemical Technology, Russian Academy of Sciences, 660049 Krasnoyarsk, Russian Federation, Faculty of Chemistry, University of Sofia, 1126 Sofia, Bulgaria, and Department Chemie, Technische Universität München, 85747 Garching, Germany
| |
Collapse
|
48
|
Casarin M, Falcomer D, Glisenti A, Natile MM, Poli F, Vittadini A. Experimental and QM/MM investigation of the hydrated silica surface reactivity. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2005.02.076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
49
|
Applications of quantum chemical methods in zeolite science. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s0167-2991(05)80014-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
50
|
Theoretical investigation of Zn-containing species in pores of ZSM-5 zeolites. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s0167-2991(05)80389-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
|