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Guan J, Lu Y, Sen K, Abdul Nasir J, Desmoutier AW, Hou Q, Zhang X, Logsdail AJ, Dutta G, Beale AM, Strange RW, Yong C, Sherwood P, Senn HM, Catlow CRA, Keal TW, Sokol AA. Computational infrared and Raman spectra by hybrid QM/MM techniques: a study on molecular and catalytic material systems. Philos Trans A Math Phys Eng Sci 2023; 381:20220234. [PMID: 37211033 PMCID: PMC10200352 DOI: 10.1098/rsta.2022.0234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/04/2023] [Indexed: 05/23/2023]
Abstract
Vibrational spectroscopy is one of the most well-established and important techniques for characterizing chemical systems. To aid the interpretation of experimental infrared and Raman spectra, we report on recent theoretical developments in the ChemShell computational chemistry environment for modelling vibrational signatures. The hybrid quantum mechanical and molecular mechanical approach is employed, using density functional theory for the electronic structure calculations and classical forcefields for the environment. Computational vibrational intensities at chemical active sites are reported using electrostatic and fully polarizable embedding environments to achieve more realistic vibrational signatures for materials and molecular systems, including solvated molecules, proteins, zeolites and metal oxide surfaces, providing useful insight into the effect of the chemical environment on the signatures obtained from experiment. This work has been enabled by the efficient task-farming parallelism implemented in ChemShell for high-performance computing platforms. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.
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Affiliation(s)
- Jingcheng Guan
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - You Lu
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington WA4 4AD, UK
| | - Kakali Sen
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington WA4 4AD, UK
| | - Jamal Abdul Nasir
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | | | - Qing Hou
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Institute of Photonic Chips, University of Shanghai for Science of Technology, Shanghai 201512, People’s Republic of China
| | - Xingfan Zhang
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Andrew J. Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
| | - Gargi Dutta
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Department of Physics, Balurghat College, Balurghat 733101, West Bengal, India
| | - Andrew M. Beale
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, UK
| | - Richard W. Strange
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Chin Yong
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington WA4 4AD, UK
| | - Paul Sherwood
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB, UK
| | - Hans M. Senn
- School of Chemistry, University of Glasgow, Joseph Black Building, Glasgow G12 8QQ, UK
| | - C. Richard A. Catlow
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, UK
| | - Thomas W. Keal
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington WA4 4AD, UK
| | - Alexey A. Sokol
- Department of Chemistry, University College London, London WC1H 0AJ, UK
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Brüggemann J, Wolter M, Jacob CR. Quantum-chemical calculation of two-dimensional infrared spectra using localized-mode VSCF/VCI. J Chem Phys 2022; 157:244107. [PMID: 36586972 DOI: 10.1063/5.0135273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Computational protocols for the simulation of two-dimensional infrared (2D IR) spectroscopy usually rely on vibrational exciton models which require an empirical parameterization. Here, we present an efficient quantum-chemical protocol for predicting static 2D IR spectra that does not require any empirical parameters. For the calculation of anharmonic vibrational energy levels and transition dipole moments, we employ the localized-mode vibrational self-consistent field (L-VSCF)/vibrational configuration interaction (L-VCI) approach previously established for (linear) anharmonic theoretical vibrational spectroscopy [P. T. Panek and C. R. Jacob, ChemPhysChem 15, 3365-3377 (2014)]. We demonstrate that with an efficient expansion of the potential energy surface using anharmonic one-mode potentials and harmonic two-mode potentials, 2D IR spectra of metal carbonyl complexes and dipeptides can be predicted reliably. We further show how the close connection between L-VCI and vibrational exciton models can be exploited to extract the parameters of such models from those calculations. This provides a novel route to the fully quantum-chemical parameterization of vibrational exciton models for predicting 2D IR spectra.
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Affiliation(s)
- Julia Brüggemann
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
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Pei Z, Mao Y, Shao Y, Liang W. Analytic high-order energy derivatives for metal nanoparticle-mediated infrared and Raman scattering spectra within the framework of quantum mechanics/molecular mechanics model with induced charges and dipoles. J Chem Phys 2022; 157:164110. [PMID: 36319412 PMCID: PMC9616608 DOI: 10.1063/5.0118205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/30/2022] [Indexed: 11/14/2022] Open
Abstract
This work is devoted to deriving and implementing analytic second- and third-order energy derivatives with respect to the nuclear coordinates and external electric field within the framework of the hybrid quantum mechanics/molecular mechanics method with induced charges and dipoles (QM/DIM). Using these analytic energy derivatives, one can efficiently compute the harmonic vibrational frequencies, infrared (IR) and Raman scattering (RS) spectra of the molecule in the proximity of noble metal clusters/nanoparticles. The validity and accuracy of these analytic implementations are demonstrated by the comparison of results obtained by the finite-difference method and the analytic approaches and by the full QM and QM/DIM calculations. The complexes formed by pyridine and two sizes of gold clusters (Au18 and Au32) at varying intersystem distances of 3, 4, and 5 Å are used as the test systems, and Raman spectra of 4,4'-bipyridine in the proximity of Au2057 and Ag2057 metal nanoparticles (MNP) are calculated by the QM/DIM method and compared with experimental results as well. We find that the QM/DIM model can well reproduce the IR spectra obtained from full QM calculations for all the configurations, while although it properly enhances some of the vibrational modes, it artificially overestimates RS spectral intensities of several modes for the systems with very short intersystem distance. We show that this could be improved, however, by incorporating the hyperpolarizability of the gold metal cluster in the evaluation of RS intensities. Additionally, we address the potential impact of charge migration between the adsorbate and MNPs.
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Affiliation(s)
- Zheng Pei
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - WanZhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
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Dundas KHM, Beerepoot MTP, Ringholm M, Reine S, Bast R, List NH, Kongsted J, Ruud K, Olsen JMH. Harmonic Infrared and Raman Spectra in Molecular Environments Using the Polarizable Embedding Model. J Chem Theory Comput 2021; 17:3599-3617. [PMID: 34009969 PMCID: PMC8278393 DOI: 10.1021/acs.jctc.0c01323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Indexed: 12/14/2022]
Abstract
We present a fully analytic approach to calculate infrared (IR) and Raman spectra of molecules embedded in complex molecular environments modeled using the fragment-based polarizable embedding (PE) model. We provide the theory for the calculation of analytic second-order geometric derivatives of molecular energies and first-order geometric derivatives of electric dipole moments and dipole-dipole polarizabilities within the PE model. The derivatives are implemented using a general open-ended response theory framework, thus allowing for an extension to higher-order derivatives. The embedding-potential parameters used to describe the environment in the PE model are derived through first-principles calculations, thus allowing a wide variety of systems to be modeled, including solvents, proteins, and other large and complex molecular environments. Here, we present proof-of-principle calculations of IR and Raman spectra of acetone in different solvents. This work is an important step toward calculating accurate vibrational spectra of molecules embedded in realistic environments.
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Affiliation(s)
- Karen
Oda Hjorth Minde Dundas
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Maarten T. P. Beerepoot
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Magnus Ringholm
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Simen Reine
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, N-0315 Oslo, Norway
| | - Radovan Bast
- Department
of Information Technology, UiT The Arctic
University of Norway, N-9037 Tromsø, Norway
| | - Nanna Holmgaard List
- Department
of Chemistry and the PULSE Institute, Stanford
University, 94305 Stanford, California, United States
- SLAC
National Accelerator Laboratory, 94025 Menlo Park, California, United States
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, DK-5230 Odense M, Denmark
| | - Kenneth Ruud
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Jógvan Magnus Haugaard Olsen
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
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