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Creutzberg J, Hedegård ED. Polarizable Embedding Complex Polarization Propagator in Four- and Two-Component Frameworks. J Chem Theory Comput 2022; 18:3671-3686. [PMID: 35549262 DOI: 10.1021/acs.jctc.1c01249] [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
Explicit embedding methods combined with the complex polarization propagator (CPP) enable the modeling of spectroscopy for increasingly complex systems with a high density of states. We present the first derivation and implementation of the CPP in four- and exact-two-component (X2C) polarizable embedding (PE) frameworks. We denote the developed methods PE-4c-CPP and PE-X2C-CPP, respectively. We illustrate the methods by estimating the solvent effect on ultraviolet-visible (UV-vis) and X-ray atomic absorption (XAS) spectra of [Rh(H2O)6]3+ and [Ir(H2O)6]3+ immersed in aqueous solution. We moreover estimate solvent effects on UV-vis spectra of a platinum complex that can be photochemically activated (in water) to kill cancer cells. Our results clearly show that the inclusion of the environment is required: UV-vis and (to a lesser degree) XAS spectra can become qualitatively different from vacuum calculations. Comparison of PE-4c-CPP and PE-X2C-CPP methods shows that X2C essentially reproduces the solvent effect obtained with the 4c methods.
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Affiliation(s)
- Joel Creutzberg
- Division of Theoretical Chemistry, Lund University, SE-223 62 Lund, Sweden
| | - Erik D Hedegård
- Division of Theoretical Chemistry, Lund University, SE-223 62 Lund, Sweden.,Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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2
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Abstract
We review recent work on property decomposition techniques using quantum chemical methods and discuss some topical applications in terms of quantum mechanics-molecular mechanics calculations and the constructing of properties of large molecules and clusters. Starting out from the so-called LoProp decomposition scheme [Gagliardi et al., J. Chem. Phys., 2004, 121, 4994] for extracting atomic and inter-atomic contributions to molecular properties we show how this method can be generalized to localized frequency-dependent polarizabilities, to localized hyperpolarizabilities and to localized dispersion coefficients. Some applications of the generalized decomposition technique are reviewed - calculations of frequency-dependent polarizabilities, Rayleigh scattering of large clusters, and calculations of hyperpolarizabilities of proteins.
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Affiliation(s)
- Hans Ågren
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Theoretical Chemistry and Biology, SE-106 91 Stockholm, Sweden.
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Wildman A, Donati G, Lipparini F, Mennucci B, Li X. Nonequilibrium Environment Dynamics in a Frequency-Dependent Polarizable Embedding Model. J Chem Theory Comput 2018; 15:43-51. [PMID: 30512961 DOI: 10.1021/acs.jctc.8b00836] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) models are some of the most powerful and computationally feasible approaches to account for solvent effects or more general environmental perturbations on quantum chemical systems. In their more recent formulations (known as polarizable embedding) they can account for electrostatic and mutual polarization effects between the QM and the MM subsystems. In this paper, a polarizable embedding scheme based on induced dipoles that is able both to describe electron evolution of the embedded QM system in an efficient manner as well as to capture the frequency dependent behavior of the solvent is proposed, namely, ωMMPol. The effects of this frequency-dependent solvent on a time-dependent model system-the Rabi oscillations of H2+ in a resonant field-are considered. The solvent is shown to introduce only mild perturbations when the excitation frequencies of the solvent and the solute are off-resonant. However, the dynamics of the H2+ are fundamentally changed in the presence of a near-resonant excitation solvent. The effectiveness of ωMMPol to simulating realistic chemical systems is demonstrated by capturing charge transfer dynamics within a solvated system.
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Affiliation(s)
- Andrew Wildman
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Greta Donati
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale , Universitá di Pisa , Via Risorgimento 35 , 56126 Pisa , Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale , Universitá di Pisa , Via Risorgimento 35 , 56126 Pisa , Italy
| | - Xiaosong Li
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
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4
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List NH, Norman P, Kongsted J, Jensen HJA. A quantum-mechanical perspective on linear response theory within polarizable embedding. J Chem Phys 2018. [PMID: 28641427 DOI: 10.1063/1.4985565] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We present a derivation of linear response theory within polarizable embedding starting from a rigorous quantum-mechanical treatment of a composite system. To this aim, two different subsystem decompositions (symmetric and nonsymmetric) of the linear response function are introduced and the pole structures as well as residues of the individual terms are discussed. In addition to providing a thorough justification for the descriptions used in polarizable embedding models, this theoretical analysis clarifies which form of the response function to use and highlights complications in separating out subsystem contributions to molecular properties. The basic features of the presented expressions and various approximate forms are illustrated by their application to a composite model system.
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Affiliation(s)
- Nanna Holmgaard List
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, Roslagstullsbacken 15, SE-106 91 Stockholm, Sweden
| | - Patrick Norman
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, Roslagstullsbacken 15, SE-106 91 Stockholm, Sweden
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Hans Jørgen Aagaard Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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Harczuk I, Nagy B, Jensen F, Vahtras O, Ågren H. Local decomposition of imaginary polarizabilities and dispersion coefficients. Phys Chem Chem Phys 2017; 19:20241-20250. [DOI: 10.1039/c7cp02399e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We present a new way to compute the two-body contribution to the dispersion energy using ab initio theory.
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Affiliation(s)
- Ignat Harczuk
- KTH Royal Institute of Technology
- School of Biotechnology
- Division of Theoretical Chemistry and Biology
- SE-106 91 Stockholm
- Sweden
| | - Balazs Nagy
- Department of Chemistry
- Aarhus University
- Langelandsgade 140
- 8000 Aarhus C
- Denmark
| | - Frank Jensen
- Department of Chemistry
- Aarhus University
- Langelandsgade 140
- 8000 Aarhus C
- Denmark
| | - Olav Vahtras
- KTH Royal Institute of Technology
- School of Biotechnology
- Division of Theoretical Chemistry and Biology
- SE-106 91 Stockholm
- Sweden
| | - Hans Ågren
- KTH Royal Institute of Technology
- School of Biotechnology
- Division of Theoretical Chemistry and Biology
- SE-106 91 Stockholm
- Sweden
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Harczuk I, Vahtras O, Ågren H. First Hyperpolarizability of Collagen Using the Point Dipole Approximation. J Phys Chem Lett 2016; 7:2132-2138. [PMID: 27203480 DOI: 10.1021/acs.jpclett.6b00721] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The application of localized hyperpolarizabilities to predict a total protein hyperpolarizability is presented for the first time, using rat-tail collagen as a demonstration example. We employ a model comprising the quadratic Applequist point-dipole approach, the so-called LoProp transformation, and a procedure with molecular fractionation using conjugate caps to determine the atomic and bond contributions to the net β tensor of the collagen [(PPG)10]3 triple-helix. By using Tholes exponential damping modification to the dyadic tensor in the Applequist equations, a correct qualitative agreement with experiment is found. The intensity of the βHRS signal and the depolarization ratios are best reproduced by decomposing the LoProp properties into the atomic positions and using Tholes exponential damping with the original damping parameter. Some ramifications of the model for general protein property optimization are briefly discussed.
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Affiliation(s)
- Ignat Harczuk
- School of Biotechnology, Division of Theoretical Chemistry and Biology, KTH Royal Institute of Technology , SE-106 91 Stockholm, Sweden
| | - Olav Vahtras
- School of Biotechnology, Division of Theoretical Chemistry and Biology, KTH Royal Institute of Technology , SE-106 91 Stockholm, Sweden
| | - Hans Ågren
- School of Biotechnology, Division of Theoretical Chemistry and Biology, KTH Royal Institute of Technology , SE-106 91 Stockholm, Sweden
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Nørby MS, Vahtras O, Norman P, Kongsted J. Assessing frequency-dependent site polarisabilities in linear response polarisable embedding. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1177667] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Morten S. Nørby
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Olav Vahtras
- KTH Royal Institute of Technology, School of Biotechnology, Division of Theoretical Chemistry and Biology, Stockholm, Sweden
| | - Patrick Norman
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
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Harczuk I, Vahtras O, Ågren H. Modeling Rayleigh Scattering of Aerosol Particles. J Phys Chem B 2016; 120:4296-301. [DOI: 10.1021/acs.jpcb.6b02278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ignat Harczuk
- School of Biotechnology,
Division of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Olav Vahtras
- School of Biotechnology,
Division of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Hans Ågren
- School of Biotechnology,
Division of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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9
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Harczuk I, Vahtras O, Ågren H. Hyperpolarizabilities of extended molecular mechanical systems. Phys Chem Chem Phys 2016; 18:8710-22. [DOI: 10.1039/c5cp06688c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The equations for decomposition of the molecular hyperpolarizabilty into atomic sites is derived alongside with equations to calculate the cluster hyperpolarizability as resulting from the second order induced dipole moments in the point-dipole model.
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Affiliation(s)
- Ignat Harczuk
- KTH Royal Institute of Technology
- School of Biotechnology
- Division of Theoretical Chemistry and Biology
- SE-106 91 Stockholm
- Sweden
| | - Olav Vahtras
- KTH Royal Institute of Technology
- School of Biotechnology
- Division of Theoretical Chemistry and Biology
- SE-106 91 Stockholm
- Sweden
| | - Hans Ågren
- KTH Royal Institute of Technology
- School of Biotechnology
- Division of Theoretical Chemistry and Biology
- SE-106 91 Stockholm
- Sweden
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10
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List NH, Olsen JMH, Kongsted J. Excited states in large molecular systems through polarizable embedding. Phys Chem Chem Phys 2016; 18:20234-50. [DOI: 10.1039/c6cp03834d] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using the polarizable embedding model enables rational design of light-sensitive functional biological materials.
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Affiliation(s)
- Nanna Holmgaard List
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense M
- Denmark
| | | | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense M
- Denmark
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