1
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Khanna A, Shedge SV, Zuehlsdorff TJ, Isborn CM. Calculating absorption and fluorescence spectra for chromophores in solution with ensemble Franck-Condon methods. J Chem Phys 2024; 161:044121. [PMID: 39077907 DOI: 10.1063/5.0217080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/03/2024] [Indexed: 07/31/2024] Open
Abstract
Accurately modeling absorption and fluorescence spectra for molecules in solution poses a challenge due to the need to incorporate both vibronic and environmental effects, as well as the necessity of accurate excited state electronic structure calculations. Nuclear ensemble approaches capture explicit environmental effects, Franck-Condon methods capture vibronic effects, and recently introduced ensemble-Franck-Condon approaches combine the advantages of both methods. In this study, we present and analyze simulated absorption and fluorescence spectra generated with combined ensemble-Franck-Condon approaches for three chromophore-solvent systems and compare them to standard ensemble and Franck-Condon spectra, as well as to the experiment. Employing configurations obtained from ground and excited state ab initio molecular dynamics, three combined ensemble-Franck-Condon approaches are directly compared to each other to assess the accuracy and relative computational time. We find that the approach employing an average finite-temperature Franck-Condon line shape generates spectra nearly identical to the direct summation of an ensemble of Franck-Condon spectra at one-fourth of the computational cost. We analyze how the spectral simulation method, as well as the level of electronic structure theory, affects spectral line shapes and associated Stokes shifts for 7-nitrobenz-2-oxa-1,3-diazol-4-yl and Nile red in dimethyl sulfoxide and 7-methoxy coumarin-4-acetic acid in methanol. For the first time, our studies show the capability of combined ensemble-Franck-Condon methods for both absorption and fluorescence spectroscopy and provide a powerful tool for simulating linear optical spectra.
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Affiliation(s)
- Ajay Khanna
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, USA
| | - Sapana V Shedge
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, USA
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Christine M Isborn
- Chemistry and Biochemistry, University of California Merced, Merced, California 95343, USA
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2
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Mashkovtsev D, Orimoto Y, Aoki Y. Fast and Accurate Calculation of the UV-Vis Spectrum with the Modified Local Excitation Approximation. J Chem Theory Comput 2023; 19:5548-5562. [PMID: 37471461 DOI: 10.1021/acs.jctc.3c00266] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
The local excitation approximation (LEA), a method for the calculation of electronic excitations localized in a specific region of a molecule, has been modified with new approaches to enhance the accuracy of the original method. The primary concept behind LEA involves isolating the region of interest as a submolecule from the full molecule using a localization method, followed by calculating electronic excitations solely within this submolecule. In this study, we examined approaches that improve the accuracy in describing the region of interest, particularly its molecular orbital energies. Additionally, the localization method was extended with a new projection technique to accelerate calculations. These approaches were studied in time-dependent density functional theory (TDDFT) calculations applied to four testing systems with a chromophore as the region of interest: two basic linear molecules, acrolein surrounded by 24 water molecules, and a model of a green fluorescent protein. For all studied systems, the results of TDDFT calculations combined with LEA exhibited near-zero error when groups of atoms adjacent to the chromophore were explicitly included in the submolecule. This was achieved with at least a quadratic speedup of the calculation time as a function of the submolecule size.
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Affiliation(s)
- Denis Mashkovtsev
- Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Yuuichi Orimoto
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Yuriko Aoki
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
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3
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Kvedaravičiūtė S, Carrasco-Busturia D, Møller KB, Olsen JMH. Polarizable Embedding without Artificial Boundary Polarization. J Chem Theory Comput 2023; 19:5122-5141. [PMID: 37458793 DOI: 10.1021/acs.jctc.3c00434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
We present a fully self-consistent polarizable embedding (PE) model that does not suffer from unphysical boundary polarization. This is achieved through the use of the minimum-image convention (MIC) in the induced electrostatics. It is a simple yet effective approach that includes a more physically accurate description of the polarization throughout the molecular system. Using PE with MIC (PE-MIC), we shed new light on the limitations of commonly employed cutoff models, such as the droplet model, when used in PE calculations. Specifically, we investigate the effects of the unphysical polarization at the outer boundary by comparing induced dipoles and the associated electrostatic potentials, as well as some optical properties of solute-solvent and biomolecular systems. We show that the magnitude of the inaccuracies caused by the unphysical polarization depends on multiple parameters: the nature of the quantum subsystem and of the environment, the cutoff model and distance, and the calculated property.
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Affiliation(s)
| | | | - Klaus B Møller
- DTU Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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4
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Bondanza M, Demoulin B, Lipparini F, Barbatti M, Mennucci B. Trajectory Surface Hopping for a Polarizable Embedding QM/MM Formulation. J Phys Chem A 2022; 126:6780-6789. [PMID: 36107729 PMCID: PMC9527758 DOI: 10.1021/acs.jpca.2c04756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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We present the implementation of trajectory surface-hopping
nonadiabatic
dynamics for a polarizable embedding QM/MM formulation. Time-dependent
density functional theory was used at the quantum mechanical level
of theory, whereas the molecular mechanics description involved the
polarizable AMOEBA force field. This implementation has been obtained
by integrating the surface-hopping program Newton-X NS with an interface
between the Gaussian 16 and the Tinker suites of codes to calculate
QM/AMOEBA energies and forces. The implementation has been tested
on a photoinduced electron-driven proton-transfer reaction involving
pyrimidine and a hydrogen-bonded water surrounded by a small cluster
of water molecules and within a large water droplet.
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Affiliation(s)
- Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | | | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Mario Barbatti
- Aix Marseille University, CNRS, ICR, 13385 Marseille, France
- Institut Universitaire de France, 75231 Paris, France
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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5
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Lafiosca P, Gómez S, Giovannini T, Cappelli C. Absorption Properties of Large Complex Molecular Systems: The DFTB/Fluctuating Charge Approach. J Chem Theory Comput 2022; 18:1765-1779. [PMID: 35184553 PMCID: PMC8908768 DOI: 10.1021/acs.jctc.1c01066] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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We report on the
first formulation of a novel polarizable QM/MM
approach, where the density functional tight binding (DFTB) is coupled
to the fluctuating charge (FQ) force field. The resulting method (DFTB/FQ)
is then extended to the linear response within the TD-DFTB framework
and challenged to study absorption spectra of large condensed-phase
systems.
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Affiliation(s)
- Piero Lafiosca
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Tommaso Giovannini
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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6
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Rossano‐Tapia M, Brown A. Quantum mechanical/molecular mechanical studies of photophysical properties of fluorescent proteins. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Alex Brown
- Department of Chemistry University of Alberta Edmonton Alberta Canada
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7
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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] [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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8
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Egidi F, Angelico S, Lafiosca P, Giovannini T, Cappelli C. A polarizable three-layer frozen density embedding/molecular mechanics approach. J Chem Phys 2021; 154:164107. [PMID: 33940798 DOI: 10.1063/5.0045574] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We present a novel multilayer polarizable embedding approach in which the system is divided into three portions, two of which are treated using density functional theory and their interaction is based on frozen density embedding (FDE) theory, and both also mutually interact with a polarizable classical layer described using an atomistic model based on fluctuating charges (FQ). The efficacy of the model is demonstrated by extending the formalism to linear response properties and applying it to the simulation of the excitation energies of organic molecules in aqueous solution, where the solute and the first solvation shell are treated using FDE, while the rest of the solvent is modeled using FQ charges.
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Affiliation(s)
- Franco Egidi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Sara Angelico
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Piero Lafiosca
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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9
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Giovannini T, Egidi F, Cappelli C. Theory and algorithms for chiroptical properties and spectroscopies of aqueous systems. Phys Chem Chem Phys 2020; 22:22864-22879. [PMID: 33043930 DOI: 10.1039/d0cp04027d] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Chiroptical properties and spectroscopies are valuable tools to study chiral molecules and assign absolute configurations. The spectra that result from chiroptical measurements may be very rich and complex, and hide much of their information content. For this reason, the interplay between experiments and calculations is especially useful, provided that all relevant physico-chemical interactions that are present in the experimental sample are accurately modelled. The inherent difficulty associated to the calculation of chiral signals of systems in aqueous solutions requires the development of specific tools, able to account for the peculiarities of water-solute interactions, and especially its ability to form hydrogen bonds. In this perspective we discuss a multiscale approach, which we have developed and challenged to model the most used chiroptical techniques.
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Affiliation(s)
- Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
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10
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Viquez Rojas CI, Slipchenko LV. Exchange Repulsion in Quantum Mechanical/Effective Fragment Potential Excitation Energies: Beyond Polarizable Embedding. J Chem Theory Comput 2020; 16:6408-6417. [PMID: 32786899 DOI: 10.1021/acs.jctc.9b01156] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hybrid quantum mechanical and molecular mechanical (QM/MM) approaches facilitate computational modeling of large biological and materials systems. Typically, in QM/MM, a small region of the system is modeled with an accurate quantum mechanical method and its surroundings with a more efficient alternative, such as a classical force field or the effective fragment potential (EFP). The reliability of QM/MM calculations depends largely on the treatment of interactions between the two subregions, also known as embedding. The polarizable embedding, which allows mutual polarization between solvent and solute, is considered to be essential for describing electronic excitations in polar solvents. In this work, we employ the QM/EFP model and extend the polarizable embedding by incorporating two short-range terms-a charge penetration correction to the electrostatic term and the exchange-repulsion term-both of which are modeled with one-electron contributions to the quantum Hamiltonian. We evaluate the accuracy of these terms by computing excitation energies across 37 molecular clusters consisting of biologically relevant chromophores surrounded by polar solvent molecules. QM/EFP excitation energies are compared to the fully quantum mechanical calculations with the configuration interaction singles (CIS) method. We find that the charge penetration correction diminishes the accuracy of the QM/EFP calculations. On the other hand, while the effect of exchange-repulsion is negligible for most ππ* transitions, the exchange-repulsion significantly improves description of nπ* transitions with blue solvatochromic shifts. As a result, addition of the exchange-repulsion term improves the overall accuracy of QM/EFP. Performances of QM/EFP models remain similar when excitation energies are modeled with cc-pVDZ and aug-cc-pVDZ basis sets.
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Affiliation(s)
- Claudia I Viquez Rojas
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
| | - Lyudmila V Slipchenko
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
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11
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Marefat Khah A, Reinholdt P, Nuernberger P, Kongsted J, Hättig C. Relaxation Dynamics of the Triazene Compound Berenil in DNA-Minor-Groove Confinement after Photoexcitation. J Chem Theory Comput 2020; 16:5203-5211. [DOI: 10.1021/acs.jctc.0c00489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense, Denmark
| | - Patrick Nuernberger
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense, Denmark
| | - Christof Hättig
- Quantum Chemistry Group, Ruhr University of Bochum, D-44780 Bochum, Germany
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12
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He N, Evangelista FA. A zeroth-order active-space frozen-orbital embedding scheme for multireference calculations. J Chem Phys 2020; 152:094107. [PMID: 33480706 DOI: 10.1063/1.5142481] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Multireference computations of large-scale chemical systems are typically limited by the computational cost of quantum chemistry methods. In this work, we develop a zeroth-order active space embedding theory [ASET(0)], a simple and automatic approach for embedding any multireference dynamical correlation method based on a frozen-orbital treatment of the environment. ASET(0) is combined with the second-order multireference driven similarity renormalization group and tested on several benchmark problems, including the excitation energy of 1-octene and bond-breaking in ethane and pentyldiazene. Finally, we apply ASET(0) to study the singlet-triplet gap of p-benzyne and 9,10-anthracyne diradicals adsorbed on a NaCl surface. Our results show that despite its simplicity, ASET(0) is a powerful and sufficiently accurate embedding scheme applicable when the coupling between the fragment and the environment is in the weak to medium regime.
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Affiliation(s)
- Nan He
- Department of Chemistry, Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Francesco A Evangelista
- Department of Chemistry, Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
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13
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Ren S, Lipparini F, Mennucci B, Caricato M. Coupled Cluster Theory with Induced Dipole Polarizable Embedding for Ground and Excited States. J Chem Theory Comput 2019; 15:4485-4496. [PMID: 31265278 DOI: 10.1021/acs.jctc.9b00468] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this work, we present the theory and implementation of the coupled cluster single and double excitations (CCSD) method combined with a classical polarizable molecular mechanics force field (MMPol) based on the induced dipole model. The method is developed to compute electronic excitation energies within the state specific (SS) and linear response (LR) formalisms for the interaction of the quantum mechanical and classical regions. Furthermore, we consider an approximate expression of the correlation energy, originally developed for CCSD with implicit solvation models, where the interaction term is linear in the coupled cluster density. This approximation allows us to include the explicit contribution of the environment to the CC equations without increasing the computational effort. The test calculations on microsolvated systems, where the CCSD/MMPol method is compared to full CCSD calculations, demonstrates the reliability of this computational protocol for all interaction schemes (errors < 2%). We also show that it is important to include induced dipoles on all atom centers of the classical region and that too diffuse functions in the basis set may be problematic due to too strong interaction with the environment.
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Affiliation(s)
- Sijin Ren
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66044 , United States
| | - Filippo Lipparini
- Department of Chemistry , Università di Pisa , Via Giuseppe Moruzzi , 13 56124 Pisa , Italy
| | - Benedetta Mennucci
- Department of Chemistry , Università di Pisa , Via Giuseppe Moruzzi , 13 56124 Pisa , Italy
| | - Marco Caricato
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66044 , United States
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14
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Lu SI. Discrete Solvent Reaction Field Calculations for One- and Two-Photon Absorptions of Solution-Phase Dimethylaminonitrostilbene Molecule. J Phys Chem A 2019; 123:5334-5340. [PMID: 31242735 DOI: 10.1021/acs.jpca.9b04041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Based on the configurations generated by molecular dynamics (MD) simulations using the on-the-fly density-functional tight-bonding (DFTB) force field, we investigated performance of the discrete solvent reaction field (DRF) model coupled to time-dependent density functional theory (TD-DFT) for solvatochromic effect of one- and two-photon absorption phenomena. Dimethylaminonitrostilbene (DANS) molecule solvated in chloroform, dichloromethane, and dimethyl sulfoxide solvents was selected as a model system for our research purpose. For every selected MD/DFTB configuration, within the context of the DRF, solute molecule is represented by TD-DFT and solvent molecules are described by atomic charges and polarizabilities. The calculated one-photon absorption energies reproduce well the positive solvatochromic behavior of solvated DANS and are in good agreement with available experimental data. For the two-photon absorption cross section, even though our approach overshot the experimental data by about 20% in absolute magnitude, experimentally observed solvatochromic change was captured qualitatively in this work. At last, we examined the contributions of atomic charges and polarizabilities of solvent molecules to the solvatochromic shifts of properties of interest.
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Affiliation(s)
- Shih-I Lu
- Department of Chemistry Soochow University No. 70 Lin-Shih Road , Taipei City , 111 , Taiwan
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15
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Stendevad J, Kongsted J, Steinmann C. Combining polarizable embedding with the Frenkel exciton model: applications to absorption spectra with overlapping solute–solvent bands. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2430-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Dziedzic J, Head-Gordon T, Head-Gordon M, Skylaris CK. Mutually polarizable QM/MM model with in situ optimized localized basis functions. J Chem Phys 2019; 150:074103. [PMID: 30795653 DOI: 10.1063/1.5080384] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with onetep linear-scaling density functional theory and the classical subsystem - with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully mutually polarizable. A total energy minimization scheme is employed for the Hamiltonian of the coupled QM/MM system. We demonstrate that, compared to simpler models using fixed basis sets, the additional flexibility offered by in situ optimized basis functions improves the accuracy of the QM/MM interface, but also poses new challenges, making the QM subsystem more prone to overpolarization and unphysical charge transfer due to increased charge penetration. We show how these issues can be efficiently solved by replacing the classical repulsive van der Waals term for QM/MM interactions with an interaction of the electronic density with a fixed, repulsive MM potential that mimics Pauli repulsion, together with a modest increase in the damping of QM/MM polarization. We validate our method, with particular attention paid to the hydrogen bond, in tests on water-ion pairs, the water dimer, first solvation shells of neutral and charged species, and solute-solvent interaction energies. As a proof of principle, we determine suitable repulsive potential parameters for water, K+, and Cl-. The mechanisms we employed to counteract the unphysical overpolarization of the QM subsystem are demonstrated to be adequate, and our approach is robust. We find that the inclusion of explicit polarization in the MM part of QM/MM improves agreement with fully QM calculations. Our model permits the use of minimal size QM regions and, remarkably, yields good energetics across the well-balanced QM/MM interface.
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Affiliation(s)
- Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Teresa Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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17
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Applications of molecular modeling to flavoproteins: Insights and challenges. Methods Enzymol 2019; 620:277-314. [DOI: 10.1016/bs.mie.2019.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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18
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19
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Hršak D, Nørby MS, Coriani S, Kongsted J. One-Photon Absorption Properties from a Hybrid Polarizable Density Embedding/Complex Polarization Propagator Approach for Polarizable Solutions. J Chem Theory Comput 2018; 14:2145-2154. [DOI: 10.1021/acs.jctc.8b00155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Dalibor Hršak
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Morten Steen Nørby
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet Building 207, 2800 Kongens Lyngby, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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20
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Schröder H, Schwabe T. Corrected Polarizable Embedding: Improving the Induction Contribution to Perichromism for Linear Response Theory. J Chem Theory Comput 2018; 14:833-842. [DOI: 10.1021/acs.jctc.7b01033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Heiner Schröder
- ZBH−Center for Bioinformatics
and Institute of Physical Chemistry, University of Hamburg, Bundesstraße
43, 20146 Hamburg, Germany
| | - Tobias Schwabe
- ZBH−Center for Bioinformatics
and Institute of Physical Chemistry, University of Hamburg, Bundesstraße
43, 20146 Hamburg, Germany
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21
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Gatto P, Lipparini F, Stamm B. Computation of forces arising from the polarizable continuum model within the domain-decomposition paradigm. J Chem Phys 2017; 147:224108. [DOI: 10.1063/1.5008329] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Paolo Gatto
- Mathematics Division, Center for Computational Engineering Science, RWTH Aachen University, Aachen, Germany
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benjamin Stamm
- Mathematics Division, Center for Computational Engineering Science, RWTH Aachen University, Aachen, Germany
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22
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Bi TJ, Xu LK, Wang F, Ming MJ, Li XY. Solvent effects on excitation energies obtained using the state-specific TD-DFT method with a polarizable continuum model based on constrained equilibrium thermodynamics. Phys Chem Chem Phys 2017; 19:32242-32252. [PMID: 29188829 DOI: 10.1039/c7cp05673g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nonequilibrium solvation effects need to be treated properly in the study of electronic absorption processes of solutes since solvent polarization is not in equilibrium with the excited-state charge density of the solute. In this work, we developed a state specific (SS) method based on the novel nonequilibrium solvation model with constrained equilibrium manipulation to account for solvation effects in electronic absorption processes. Time-dependent density functional theory (TD-DFT) is adopted to calculate electronic excitation energies and a polarizable continuum model is employed in the treatment of bulk solvent effects on both the ground and excited electronic states. The equations based on this novel nonequilibrium solvation model in the framework of TDDFT to calculate vertical excitation energy are presented and implemented in the Q-Chem package. The implementation is validated by comparing reorganization energies for charge transfer excitations between two atoms obtained from Q-Chem and those obtained using a two-sphere model. Solvent effects on electronic transitions of coumarin 153 (C153), acetone, pyridine, (2E)-3-(3,4-dimethoxyphenyl)-1-(2-hydroxyphenyl)prop-2-en-1-one (DMHP), and uracil in different solvents are investigated using the newly developed code. Our results show that the obtained vertical excitation energies as well as spectral shifts generally agree better with the available experimental values than those obtained using the traditional nonequlibrium solvation model. This new model is thus appropriate to study nonequilibrium excitation processes in solution.
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Affiliation(s)
- Ting-Jun Bi
- College of Chemical Engineering, Sichuan University, Chengdu 610065, China.
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23
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Abstract
The dispersion energy term between quantum-mechanical (QM) and classical (represented by effective fragment potentials, EFP) subsystems is developed and implemented. A new formulation is based on long-range perturbation theory and uses dynamic polarizability tensors of the effective fragments and electric field integrals and orbital energies of the quantum-mechanical subsystem. No parametrization is involved. The accuracy of the QM-EFP dispersion energy is tested on a number of model systems; the average mean unsigned error is 0.8 kcal/mol or 13% with respect to the symmetry adapted perturbation theory on the S22 data set of noncovalent interactions. The computational cost of the dispersion energy computation is low compared to the self-consistent field calculation of the QM subsystem. The dispersion energy is sensitive to the level of theory employed for the QM part and to the electrostatic interactions in the system. The latter means that the dispersion interactions in the QM/EFP method are not purely two-body but have more complex many-body behavior.
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Affiliation(s)
- Lyudmila V Slipchenko
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University , Ames, Iowa 50011, United States
| | - Klaus Ruedenberg
- Department of Chemistry and Ames Laboratory, Iowa State University , Ames, Iowa 50011, United States
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24
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Hršak D, Olsen JMH, Kongsted J. Optimization and transferability of non-electrostatic repulsion in the polarizable density embedding model. J Comput Chem 2017. [DOI: 10.1002/jcc.24859] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dalibor Hršak
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 Odense M 5230 Denmark
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 Odense M 5230 Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 Odense M 5230 Denmark
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25
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Mao Y, Shao Y, Dziedzic J, Skylaris CK, Head-Gordon T, Head-Gordon M. Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis. J Chem Theory Comput 2017; 13:1963-1979. [PMID: 28430427 DOI: 10.1021/acs.jctc.7b00089] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized with respect to both the QM electronic density and the MM induced dipoles. This QM/AMOEBA model is implemented through the Q-Chem/LibEFP code interface and then applied to the evaluation of solute-solvent interaction energies for various systems ranging from the water dimer to neutral and ionic solutes (NH3, NH4+, CN-) surrounded by increasing numbers of water molecules (up to 100). In order to analyze the resulting interaction energies, we also utilize an energy decomposition analysis (EDA) scheme which identifies contributions from permanent electrostatics, polarization, and van der Waals (vdW) interaction for the interaction between the QM solute and the solvent molecules described by AMOEBA. This facilitates a component-wise comparison against full QM calculations where the corresponding energy components are obtained via a modified version of the absolutely localized molecular orbitals (ALMO)-EDA. The results show that the present QM/AMOEBA model can yield reasonable solute-solvent interaction energies for neutral and cationic species, while further scrutiny reveals that this accuracy highly relies on the delicate balance between insufficiently favorable permanent electrostatics and softened vdW interaction. For anionic solutes where the charge penetration effect becomes more pronounced, the QM/MM interface turns out to be unbalanced. These results are consistent with and further elucidate our findings in a previous study using a slightly different QM/AMOEBA model ( Dziedzic et al. J. Chem. Phys. 2016 , 145 , 124106 ). The implications of these results for further refinement of this model are also discussed.
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Affiliation(s)
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K.,Faculty of Applied Physics and Mathematics, Gdańsk University of Technology , Gdańsk 80-233, Poland
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
| | | | - Martin Head-Gordon
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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26
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Pagliai M, Mancini G, Carnimeo I, De Mitri N, Barone V. Electronic absorption spectra of pyridine and nicotine in aqueous solution with a combined molecular dynamics and polarizable QM/MM approach. J Comput Chem 2017; 38:319-335. [PMID: 27910109 PMCID: PMC6680224 DOI: 10.1002/jcc.24683] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/04/2016] [Accepted: 11/08/2016] [Indexed: 01/06/2023]
Abstract
The electronic absorption spectra of pyridine and nicotine in aqueous solution have been computed using a multistep approach. The computational protocol consists in studying the solute solvation with accurate molecular dynamics simulations, characterizing the hydrogen bond interactions, and calculating electronic transitions for a series of configurations extracted from the molecular dynamics trajectories with a polarizable QM/MM scheme based on the fluctuating charge model. Molecular dynamics simulations and electronic transition calculations have been performed on both pyridine and nicotine. Furthermore, the contributions of solute vibrational effect on electronic absorption spectra have been taken into account in the so called vertical gradient approximation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Marco Pagliai
- Scuola Normale SuperiorePiazza dei Cavalieri 7PisaI‐56126Italy
| | | | - Ivan Carnimeo
- Scuola Normale SuperiorePiazza dei Cavalieri 7PisaI‐56126Italy
- Compunet, Istituto Italiano di Tecnologia (IIT)via Morego 30GenovaI‐16163Italy
| | - Nicola De Mitri
- Scuola Normale SuperiorePiazza dei Cavalieri 7PisaI‐56126Italy
- Present address:
Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWU.K.
| | - Vincenzo Barone
- Scuola Normale SuperiorePiazza dei Cavalieri 7PisaI‐56126Italy
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27
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Nocito D, Beran GJO. Averaged Condensed Phase Model for Simulating Molecules in Complex Environments. J Chem Theory Comput 2017; 13:1117-1129. [PMID: 28170251 DOI: 10.1021/acs.jctc.6b00890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The need for configurational sampling dramatically increases the cost of combined quantum mechanics/molecular mechanics (QM/MM) simulations of chemical processes in solution. We developed an averaged condensed phase environment (ACPE) model that constructs an effective polarizable environment directly from explicitly sampled molecular dynamics configurations via the K-means++ algorithm and a mathematically rigorous translation of the molecular mechanics parameters. The model captures detailed heterogeneous features in the environment that may be difficult to describe using a conventional polarizable continuum model. Instead of performing repeated QM/MM calculations for each new configuration of the environment, the ACPE approach allows one to perform a single QM calculation on an averaged configuration. Here, we demonstrate the model by computing electronic excitation energies for several small molecules in solution. The ACPE model predicts the excitation energies in excellent agreement with conventional configurational averaging yet with orders of magnitude of reduction in the computational cost.
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Affiliation(s)
- Dominique Nocito
- Department of Chemistry, University of California , Riverside, California 92521, United States
| | - Gregory J O Beran
- Department of Chemistry, University of California , Riverside, California 92521, United States
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28
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Witzke S, List NH, Olsen JMH, Steinmann C, Petersen M, Beerepoot MTP, Kongsted J. An averaged polarizable potential for multiscale modeling in phospholipid membranes. J Comput Chem 2017; 38:601-611. [PMID: 28160294 DOI: 10.1002/jcc.24718] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 12/07/2016] [Accepted: 12/09/2016] [Indexed: 01/28/2023]
Abstract
A set of average atom-centered charges and polarizabilities has been developed for three types of phospholipids for use in polarizable embedding calculations. The lipids investigated are 1,2-dimyristoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, and 1-palmitoyl-2-oleoyl-sn-glycerol-3-phospho-L-serine given their common use both in experimental and computational studies. The charges, and to a lesser extent the polarizabilities, are found to depend strongly on the molecular conformation of the lipids. Furthermore, the importance of explicit polarization is underlined for the description of larger assemblies of lipids, that is, membranes. In conclusion, we find that specially developed polarizable parameters are needed for embedding calculations in membranes, while common non-polarizable point-charge force fields usually perform well enough for structural and dynamical studies. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Sarah Witzke
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, DK-5230, Denmark
| | - Nanna Holmgaard List
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | | | - Casper Steinmann
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Michael Petersen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, DK-5230, Denmark
| | - Maarten T P Beerepoot
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, Tromsø, N-9037, Norway
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, DK-5230, Denmark
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29
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Steinmann C, Bratholm LA, Olsen JMH, Kongsted J. Automated Fragmentation Polarizable Embedding Density Functional Theory (PE-DFT) Calculations of Nuclear Magnetic Resonance (NMR) Shielding Constants of Proteins with Application to Chemical Shift Predictions. J Chem Theory Comput 2017; 13:525-536. [PMID: 27992211 DOI: 10.1021/acs.jctc.6b00965] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Full-protein nuclear magnetic resonance (NMR) shielding constants based on ab initio calculations are desirable, because they can assist in elucidating protein structures from NMR experiments. In this work, we present NMR shielding constants computed using a new automated fragmentation (J. Phys. Chem. B 2009, 113, 10380-10388) approach in the framework of polarizable embedding density functional theory. We extend our previous work to give both basis set recommendations and comment on how large the quantum mechanical region should be to successfully compute 13C NMR shielding constants that are comparable with experiment. The introduction of a probabilistic linear regression model allows us to substantially reduce the number of snapshots that are needed to make comparisons with experiment. This approach is further improved by augmenting snapshot selection with chemical shift predictions by which we can obtain a representative subset of snapshots that gives the smallest predicted error, compared to experiment. Finally, we use this subset of snapshots to calculate the NMR shielding constants at the PE-KT3/pcSseg-2 level of theory for all atoms in the protein GB3.
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Affiliation(s)
- Casper Steinmann
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol BS8 1TS, United Kingdom.,Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , DK-5230 Odense M, Denmark
| | | | | | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , DK-5230 Odense M, Denmark
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30
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Schwabe T. General theory for environmental effects on (vertical) electronic excitation energies. J Chem Phys 2016; 145:154105. [DOI: 10.1063/1.4964321] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Eilmes A, Kubisiak P, Brela M. Explicit Solvent Modeling of IR and UV–Vis Spectra of 1-Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide Ionic Liquid. J Phys Chem B 2016; 120:11026-11034. [DOI: 10.1021/acs.jpcb.6b07994] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrzej Eilmes
- Faculty of Chemistry, Jagiellonian University, Ingardena
3, 30-060 Kraków, Poland
| | - Piotr Kubisiak
- Faculty of Chemistry, Jagiellonian University, Ingardena
3, 30-060 Kraków, Poland
| | - Mateusz Brela
- Faculty of Chemistry, Jagiellonian University, Ingardena
3, 30-060 Kraków, Poland
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32
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Dziedzic J, Mao Y, Shao Y, Ponder J, Head-Gordon T, Head-Gordon M, Skylaris CK. TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field. J Chem Phys 2016; 145:124106. [DOI: 10.1063/1.4962909] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Gdańsk, Poland
| | - Yuezhi Mao
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yihan Shao
- Q-Chem Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Jay Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
- Department of Bioengineering, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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33
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Nørby MS, Steinmann C, Olsen JMH, Li H, Kongsted J. Computational Approach for Studying Optical Properties of DNA Systems in Solution. J Chem Theory Comput 2016; 12:5050-5057. [DOI: 10.1021/acs.jctc.6b00706] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Morten Steen Nørby
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Casper Steinmann
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | | | - Hui Li
- Department
of Chemistry and Nebraska Center for Materials and Nanoscience, University of Nebraska—Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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34
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Megow J. Computing dispersive, polarizable, and electrostatic shifts of excitation energy in supramolecular systems: PTCDI crystal. J Chem Phys 2016; 145:094109. [DOI: 10.1063/1.4962179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Jörg Megow
- Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Straße 24-25, D-14476 Potsdam, Federal Republic of Germany
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35
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Hedegård ED, Reiher M. Polarizable Embedding Density Matrix Renormalization Group. J Chem Theory Comput 2016; 12:4242-53. [PMID: 27537835 DOI: 10.1021/acs.jctc.6b00476] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The polarizable embedding (PE) approach is a flexible embedding model where a preselected region out of a larger system is described quantum mechanically, while the interaction with the surrounding environment is modeled through an effective operator. This effective operator represents the environment by atom-centered multipoles and polarizabilities derived from quantum mechanical calculations on (fragments of) the environment. Thereby, the polarization of the environment is explicitly accounted for. Here, we present the coupling of the PE approach with the density matrix renormalization group (DMRG). This PE-DMRG method is particularly suitable for embedded subsystems that feature a dense manifold of frontier orbitals which requires large active spaces. Recovering such static electron-correlation effects in multiconfigurational electronic structure problems, while accounting for both electrostatics and polarization of a surrounding environment, allows us to describe strongly correlated electronic structures in complex molecular environments. We investigate various embedding potentials for the well-studied first excited state of water with active spaces that correspond to a full configuration-interaction treatment. Moreover, we study the environment effect on the first excited state of a retinylidene Schiff base within a channelrhodopsin protein. For this system, we also investigate the effect of dynamical correlation included through short-range density functional theory.
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Affiliation(s)
- Erik D Hedegård
- Laboratorium für Physikalische Chemie, ETH Zürich , Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zürich , Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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36
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Schröder H, Schwabe T. Efficient determination of accurate atomic polarizabilities for polarizeable embedding calculations. J Comput Chem 2016; 37:2052-9. [PMID: 27317509 PMCID: PMC5094558 DOI: 10.1002/jcc.24425] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/03/2016] [Accepted: 05/23/2016] [Indexed: 12/16/2022]
Abstract
We evaluate embedding potentials, obtained via various methods, used for polarizable embedding computations of excitation energies of para-nitroaniline in water and organic solvents as well as of the green fluorescent protein. We found that isotropic polarizabilities derived from DFTD3 dispersion coefficients correlate well with those obtained via the LoProp method. We show that these polarizabilities in conjunction with appropriately derived point charges are in good agreement with calculations employing static multipole moments up to quadrupoles and anisotropic polarizabilities for both computed systems. The (partial) use of these easily-accessible parameters drastically reduces the computational effort to obtain accurate embedding potentials especially for proteins. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Heiner Schröder
- Center for Bioinformatics and Institute of Physical Chemistry, University of Hamburg, Bundesstraße 43, Hamburg, 20146, Germany
| | - Tobias Schwabe
- Center for Bioinformatics and Institute of Physical Chemistry, University of Hamburg, Bundesstraße 43, Hamburg, 20146, Germany
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37
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Junager NPL, Kongsted J, Astakhova K. Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes. SENSORS (BASEL, SWITZERLAND) 2016; 16:E1173. [PMID: 27472344 PMCID: PMC5017339 DOI: 10.3390/s16081173] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 01/08/2023]
Abstract
Nucleic acid mutations are of tremendous importance in modern clinical work, biotechnology and in fundamental studies of nucleic acids. Therefore, rapid, cost-effective and reliable detection of mutations is an object of extensive research. Today, Förster resonance energy transfer (FRET) probes are among the most often used tools for the detection of nucleic acids and in particular, for the detection of mutations. However, multiple parameters must be taken into account in order to create efficient FRET probes that are sensitive to nucleic acid mutations. In this review; we focus on the design principles for such probes and available computational methods that allow for their rational design. Applications of advanced, rationally designed FRET probes range from new insights into cellular heterogeneity to gaining new knowledge of nucleic acid structures directly in living cells.
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Affiliation(s)
- Nina P L Junager
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Kira Astakhova
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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38
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S. Nørby M, Magnus Haugaard Olsen J, Kongsted J, Aagard Jensen HJ. Multipole moments for embedding potentials: Exploring different atomic allocation algorithms. J Comput Chem 2016; 37:1887-96. [DOI: 10.1002/jcc.24403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/07/2016] [Accepted: 04/13/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Morten S. Nørby
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark, DK-5230 Odense M, Denmark
- Department of Physics; Chemistry and Biology, Linköping University; Linköping SE 58183 Sweden
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; DK-5230 Odense M Denmark
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale De Lausanne (EPFL); Lausanne CH-1015 Switzerland
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Hans Jørgen Aagard Jensen
- Department of Physics, Chemistry and Pharmacy; University of Southern Denmark, DK-5230 Odense M, Denmark
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39
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Kratz EG, Walker AR, Lagardère L, Lipparini F, Piquemal JP, Cisneros GA. LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields. J Comput Chem 2016; 37:1019-29. [PMID: 26781073 PMCID: PMC4808410 DOI: 10.1002/jcc.24295] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 09/21/2015] [Accepted: 12/17/2015] [Indexed: 12/23/2022]
Abstract
We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER-HP to enable QM/MM calculations using multipolar/polarizable force fields. LICHEM extracts forces and energies from unmodified QM and MM software packages to perform geometry optimizations, single-point energy calculations, or Monte Carlo simulations. When the QM and MM regions are connected by covalent bonds, the pseudo-bond approach is employed to smoothly transition between the QM region and the polarizable force field. A series of water clusters and small peptides have been employed to test our initial implementation. The results obtained from these test systems show the capabilities of the new software and highlight the importance of including explicit polarization. © 2016 Wiley Periodicals, Inc.
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40
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Guareschi R, Zulfikri H, Daday C, Floris FM, Amovilli C, Mennucci B, Filippi C. Introducing QMC/MMpol: Quantum Monte Carlo in Polarizable Force Fields for Excited States. J Chem Theory Comput 2016; 12:1674-83. [DOI: 10.1021/acs.jctc.6b00044] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Riccardo Guareschi
- MESA+
Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Habiburrahman Zulfikri
- MESA+
Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Csaba Daday
- MESA+
Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Franca Maria Floris
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe
Moruzzi 13, 56124 Pisa, Italy
| | - Claudio Amovilli
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe
Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe
Moruzzi 13, 56124 Pisa, Italy
| | - Claudia Filippi
- MESA+
Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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41
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Beerepoot MTP, Steindal AH, List NH, Kongsted J, Olsen JMH. Averaged Solvent Embedding Potential Parameters for Multiscale Modeling of Molecular Properties. J Chem Theory Comput 2016; 12:1684-95. [PMID: 26938368 DOI: 10.1021/acs.jctc.5b01000] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We derive and validate averaged solvent parameters for embedding potentials to be used in polarizable embedding quantum mechanics/molecular mechanics (QM/MM) molecular property calculations of solutes in organic solvents. The parameters are solvent-specific atom-centered partial charges and isotropic polarizabilities averaged over a large number of geometries of solvent molecules. The use of averaged parameters reduces the computational cost to obtain the embedding potential, which can otherwise be a rate-limiting step in calculations involving large environments. The parameters are evaluated by analyzing the quality of the resulting molecular electrostatic potentials with respect to full QM potentials. We show that a combination of geometry-specific parameters for solvent molecules close to the QM region and averaged parameters for solvent molecules further away allows for efficient polarizable embedding multiscale modeling without compromising the accuracy. The results are promising for the development of general embedding parameters for biomolecules, where the reduction in computational cost can be considerable.
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Affiliation(s)
- Maarten T P Beerepoot
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway , N-9037 Tromsø, Norway
| | - Arnfinn Hykkerud Steindal
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway , N-9037 Tromsø, Norway
| | - Nanna Holmgaard List
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , DK-5230 Odense M, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , DK-5230 Odense M, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , DK-5230 Odense M, Denmark.,Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
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42
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Steindal AH, Beerepoot MTP, Ringholm M, List NH, Ruud K, Kongsted J, Olsen JMH. Open-ended response theory with polarizable embedding: multiphoton absorption in biomolecular systems. Phys Chem Chem Phys 2016; 18:28339-28352. [DOI: 10.1039/c6cp05297e] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present the theory and implementation of an open-ended framework for electric response properties that includes effects from the molecular environment modeled by the polarizable embedding model.
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Affiliation(s)
- Arnfinn Hykkerud Steindal
- Centre of Theoretical and Computational Chemistry
- Department of Chemistry
- University of Tromsø—The Arctic University of Norway
- N-9037 Tromsø
- Norway
| | - Maarten T. P. Beerepoot
- Centre of Theoretical and Computational Chemistry
- Department of Chemistry
- University of Tromsø—The Arctic University of Norway
- N-9037 Tromsø
- Norway
| | - Magnus Ringholm
- Centre of Theoretical and Computational Chemistry
- Department of Chemistry
- University of Tromsø—The Arctic University of Norway
- N-9037 Tromsø
- Norway
| | - Nanna Holmgaard List
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- DK-5230 Odense
- Denmark
| | - Kenneth Ruud
- Centre of Theoretical and Computational Chemistry
- Department of Chemistry
- University of Tromsø—The Arctic University of Norway
- N-9037 Tromsø
- Norway
| | - Jacob Kongsted
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- DK-5230 Odense
- Denmark
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43
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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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44
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Carnimeo I, Cappelli C, Barone V. Analytical gradients for MP2, double hybrid functionals, and TD-DFT with polarizable embedding described by fluctuating charges. J Comput Chem 2015; 36:2271-90. [PMID: 26399473 PMCID: PMC5054946 DOI: 10.1002/jcc.24195] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 07/31/2015] [Accepted: 08/07/2015] [Indexed: 01/09/2023]
Abstract
A polarizable quantum mechanics (QM)/ molecular mechanics (MM) approach recently developed for Hartree-Fock (HF) and Kohn-Sham (KS) methods has been extended to energies and analytical gradients for MP2, double hybrid functionals, and TD-DFT models, thus allowing the computation of equilibrium structures for excited electronic states together with more accurate results for ground electronic states. After a detailed presentation of the theoretical background and of some implementation details, a number of test cases are analyzed to show that the polarizable embedding model based on fluctuating charges (FQ) is remarkably more accurate than the corresponding electronic embedding based on a fixed charge (FX) description. In particular, a set of electronegativities and hardnesses has been optimized for interactions between QM and FQ regions together with new repulsion-dispersion parameters. After validation of both the numerical implementation and of the new parameters, absorption electronic spectra have been computed for representative model systems including vibronic effects. The results show remarkable agreement with full QM computations and significant improvement with respect to the corresponding FX results. The last part of the article provides some hints about computation of solvatochromic effects on absorption spectra in aqueous solution as a function of the number of FQ water molecules and on the use of FX external shells to improve the convergence of the results. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Ivan Carnimeo
- Istituto Italiano Di Tecnologia (IIT), Compunet, via Morego, 30 I-16163 Genova, Italy and Scuola Normale Superiore, Piazza Dei Cavalieri, 7 I-56126, Pisa, Italy
| | - Chiara Cappelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi, 13, I-56124, Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri, 7 I-56126, Pisa, Italy
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45
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Eilmes A, Kubisiak P. Explicit Solvent Modeling of Solvatochromic Probes in Ionic Liquids: Implications of Solvation Shell Structure. J Phys Chem B 2015; 119:13185-97. [DOI: 10.1021/acs.jpcb.5b07767] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrzej Eilmes
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland
| | - Piotr Kubisiak
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland
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46
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List NH, Beerepoot MTP, Olsen JMH, Gao B, Ruud K, Jensen HJA, Kongsted J. Molecular quantum mechanical gradients within the polarizable embedding approach--application to the internal vibrational Stark shift of acetophenone. J Chem Phys 2015; 142:034119. [PMID: 25612701 DOI: 10.1063/1.4905909] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We present an implementation of analytical quantum mechanical molecular gradients within the polarizable embedding (PE) model to allow for efficient geometry optimizations and vibrational analysis of molecules embedded in large, geometrically frozen environments. We consider a variational ansatz for the quantum region, covering (multiconfigurational) self-consistent-field and Kohn-Sham density functional theory. As the first application of the implementation, we consider the internal vibrational Stark effect of the C=O group of acetophenone in different solvents and derive its vibrational linear Stark tuning rate using harmonic frequencies calculated from analytical gradients and computed local electric fields. Comparisons to PE calculations employing an enlarged quantum region as well as to a non-polarizable embedding scheme show that the inclusion of mutual polarization between acetophenone and water is essential in order to capture the structural modifications and the associated frequency shifts observed in water. For more apolar solvents, a proper description of dispersion and exchange-repulsion becomes increasingly important, and the quality of the optimized structures relies to a larger extent on the quality of the Lennard-Jones parameters.
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Affiliation(s)
- Nanna Holmgaard List
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M, Odense DK-5230 Denmark
| | - Maarten T P Beerepoot
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M, Odense DK-5230 Denmark
| | - Bin Gao
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Hans Jørgen Aagaard Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M, Odense DK-5230 Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M, Odense DK-5230 Denmark
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47
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Abstract
For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied.
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Affiliation(s)
- Tobias Schwabe
- Center for Bioinformatics and Physical Chemistry Institute, University of Hamburg, Bundesstraße 43, D-20146 Hamburg, Germany
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48
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Olsen JMH, List NH, Kristensen K, Kongsted J. Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials. J Chem Theory Comput 2015; 11:1832-42. [DOI: 10.1021/acs.jctc.5b00078] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jógvan Magnus Haugaard Olsen
- Laboratory
of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Nanna Holmgaard List
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Kasper Kristensen
- qLEAP
Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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49
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Hedegård ED, Olsen JMH, Knecht S, Kongsted J, Jensen HJA. Polarizable embedding with a multiconfiguration short-range density functional theory linear response method. J Chem Phys 2015; 142:114113. [DOI: 10.1063/1.4914922] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Erik Donovan Hedegård
- Laboratorium fur Physikalische Chemie, ETH Zürich, Vladimir Prelog Weg 2, CH-8093 Zürich, Switzerland
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Stefan Knecht
- Laboratorium fur Physikalische Chemie, ETH Zürich, Vladimir Prelog Weg 2, CH-8093 Zürich, Switzerland
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Hans Jørgen Aagaard Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
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50
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Olsen JMH, Steinmann C, Ruud K, Kongsted J. Polarizable Density Embedding: A New QM/QM/MM-Based Computational Strategy. J Phys Chem A 2015; 119:5344-55. [DOI: 10.1021/jp510138k] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jógvan Magnus Haugaard Olsen
- Laboratory of
Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense
M, Denmark
| | - Casper Steinmann
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense
M, Denmark
| | - Kenneth Ruud
- Centre for Theoretical
and Computational Chemistry, Department of Chemistry, University of Tromsø—The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense
M, Denmark
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