1
|
Creutzberg J, Hedegård ED. A method to capture the large relativistic and solvent effects on the UV-vis spectra of photo-activated metal complexes. Phys Chem Chem Phys 2023; 25:6153-6163. [PMID: 36752122 DOI: 10.1039/d2cp04937f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We have recently developed a method based on relativistic time-dependent density functional theory (TD-DFT) that allows the calculation of electronic spectra in solution (Creutzberg, Hedegård, J. Chem. Theory Comput.18, 2022, 3671). This method treats the solvent explicitly with a classical, polarizable embedding (PE) description. Furthermore, it employs the complex polarization propagator (CPP) formalism which allows calculations on complexes with a dense population of electronic states (such complexes are known to be problematic for conventional TD-DFT). Here, we employ this method to investigate both the dynamic and electronic effects of the solvent for the excited electronic states of trans-trans-trans-[Pt(N3)2(OH)2(NH3)2] in aqueous solution. This complex decomposes into species harmful to cancer cells under light irradiation. Thus, understanding its photo-physical properties may lead to a more efficient method to battle cancer. We quantify the effect of the underlying structure and dynamics by classical molecular mechanics simulations, refined with a subsequent DFT or semi-empirical optimization on a cluster. Moreover, we quantify the effect of employing different methods to set up the solvated system, e.g., how sensitive the results are to the method used for the refinement, and how large a solvent shell that is required. The electronic solvent effect is always included through a PE potential.
Collapse
Affiliation(s)
- Joel Creutzberg
- Division of Theoretical Chemistry, Lund University, Lund, Sweden.
| | - Erik Donovan Hedegård
- Division of Theoretical Chemistry, Lund University, Lund, Sweden. .,Department of Physics, Chemistry and Pharmacy, Campusvej 55, 5230 Odense, Denmark.
| |
Collapse
|
2
|
Jørgensen FK, Reinholdt P, Hedegård ED, Kongsted J. Nuclear Magnetic Shielding Constants with the Polarizable Density Embedding Model. J Chem Theory Comput 2022; 18:7384-7393. [PMID: 36332108 DOI: 10.1021/acs.jctc.2c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We extend the polarizable density embedding (PDE) model to support the calculation of nuclear magnetic resonance (NMR) shielding constants using gauge-including atomic orbitals (GIAOs) within a density functional theory (DFT) framework. The PDE model divides the total system into fragments, describing some by quantum mechanics (QM) and the others through an embedding model. The PDE model uses anisotropic polarizabilities, inter-fragment two-electron Coulomb integrals, and a non-local repulsion operator to emulate the QM effects. The terms involving Coulomb integrals are straightforwardly extended with GIAOs. In contrast, we consider two approaches to handle the gauge dependency of the non-local operator, employing either simple symmetrization or a gauge transformation. We find the latter approach to be most stable with respect to increasing the basis set size of the QM region. We examine the accuracy of the PDE model for calculating NMR shielding constants on several solutes in a water solution. The performance is compared with the classical polarizable embedding (PE) model in addition to supermolecular reference calculations. Based on these systems, we address the basis set convergence characteristics and the QM region size requirements. Furthermore, we investigate the performance of the PDE model for a system with significant electron spill-out. In many cases, we find that the PDE model outperforms the PE model, especially regarding the accuracy of nuclear shielding constants when using small QM region sizes and in systems with significant electron spill-out.
Collapse
Affiliation(s)
- Frederik Kamper Jørgensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230Odense M, Denmark
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230Odense M, Denmark
| | - Erik Donovan Hedegård
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230Odense M, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230Odense M, Denmark
| |
Collapse
|
3
|
Liu X, Humeniuk A, Glover WJ. Conical Intersections in Solution with Polarizable Embedding: Integral-Exact Direct Reaction Field. J Chem Theory Comput 2022; 18:6826-6839. [PMID: 36251342 DOI: 10.1021/acs.jctc.2c00662] [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
A common strategy to exploring the properties and reactivity of complex systems is to use quantum mechanics/molecular mechanics (QM/MM) embedding, wherein a QM region is defined and treated with electronic structure theory, and the remainder of the system is treated with a force field. Important to the description of electronic excited states, especially those of charge-transfer character, is the treatment of the coupling between the QM and MM subsystems. The state of the art is to use a polarizable force field for the MM region and mutually couple the QM wavefunction and MM induced dipoles, in addition to the usual electrostatic embedding, yielding a polarizable embedding (QM/MM-Pol) approach. However, we showed previously that current popular QM/MM-Pol approaches exhibit issues of root flipping and/or incorrect descriptions of electronic crossings in multistate calculations [J. Chem. Theory Comput. 14, 2137 (2018)]. Here, we demonstrate a solution to these problems with an integral-exact reformulation of the direct reaction field approach of Thole and Van Duijnen (QM/MM-IEDRF). The resulting embedding potential includes one- and two-electron operators and many-body dipole-induced dipole interactions and thus includes a natural description of the screening of electron-electron interactions by the MM induced dipoles. Pauli repulsion from the environment is mimicked by effective core potentials on the MM atoms. Inherent to the DRF approach is the assumption that MM dipoles respond instantaneously to the positions of the QM electrons; therefore, dispersion interactions are captured approximately. All electronic states are eigenfunctions of the same Hamiltonian, while the polarization induced in the environment and the associated energetic stabilization are unique to each state. This allows for a consistent definition of transition properties and state crossings. We demonstrate QM/MM-IEDRF by exploring the influence of a (polarizable) inert xenon matrix environment on the conical intersection underlying the photoisomerization of ethylene.
Collapse
Affiliation(s)
- Xiao Liu
- NYU Shanghai, 1555 Century Avenue, Shanghai200122, China
| | - Alexander Humeniuk
- NYU Shanghai, 1555 Century Avenue, Shanghai200122, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai200062, China
| | - William J Glover
- NYU Shanghai, 1555 Century Avenue, Shanghai200122, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai200062, China.,Department of Chemistry, New York University, New York, New York10003, United States
| |
Collapse
|
4
|
Van den Heuvel W, Reinholdt P, Jensen HJA, Kongsted J. Multiconfigurational SCF and Short-Range DFT Combined with Polarizable Density Embedding: Comparison of Linear-Response and State-Specific Solvatochromic Shifts of Acrolein and Para-nitrophenolate in Water. J Chem Theory Comput 2022; 18:6231-6239. [PMID: 36131620 DOI: 10.1021/acs.jctc.2c00739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The polarizable density embedding model is combined with the multiconfigurational self-consistent field and MC-srDFT electronic structure methods to calculate solvatochromic shifts of the n-π* absorption of acrolein and the π-π* absorption of the para-nitrophenolate anion in aqueous solution. Differences between linear-response (LR) and state-specific (SS) solvent shifts are analyzed by assessing the contributions of different terms in the solvent potential. This comparison shows that the differences are not only due to the intrinsically different response of LR and SS excitation energies to the polarizability of the environment but also due to a different response to the static part of the environment potential. These observations show that even in nonpolarizable environments, LR and SS calculations based on SCF (orbital optimization) methods do not necessarily agree on the spectral shift. The difference can be as large as, or even dominate, the difference due to dynamical polarization.
Collapse
Affiliation(s)
- Willem Van den Heuvel
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Hans Jørgen Aa Jensen
- 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
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Wang Z, Liu W. iOI: An Iterative Orbital Interaction Approach for Solving the Self-Consistent Field Problem. J Chem Theory Comput 2021; 17:4831-4845. [PMID: 34240856 DOI: 10.1021/acs.jctc.1c00445] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An iterative orbital interaction (iOI) approach is proposed to solve, in a bottom-up fashion, the self-consistent field problem in quantum chemistry. While it belongs grossly to the family of fragment-based quantum chemical methods, iOI is distinctive in that (1) it divides and conquers not only the energy but also the wave function and that (2) the subsystem sizes are automatically determined by successively merging neighboring small subsystems until they are just enough for converging the wave function to a given accuracy. Orthonormal occupied and virtual localized molecular orbitals are obtained in a natural manner, which can be used for all post-SCF purposes.
Collapse
Affiliation(s)
- Zikuan Wang
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, P. R. China
| |
Collapse
|
7
|
Loco D, Lagardère L, Adjoua O, Piquemal JP. Atomistic Polarizable Embeddings: Energy, Dynamics, Spectroscopy, and Reactivity. Acc Chem Res 2021; 54:2812-2822. [PMID: 33961401 PMCID: PMC8264944 DOI: 10.1021/acs.accounts.0c00662] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Indexed: 12/20/2022]
Abstract
The computational modeling of realistic extended systems, relevant in, e.g., Chemistry and Biophysics, is a fundamental problem of paramount importance in contemporary research. Enzymatic catalysis and photoinduced processes in pigment-protein complexes are typical problems targeted by computer-aided approaches, to complement experiments as interpretative tools at a molecular scale. The daunting complexity of this task lies in between the opposite stringent requirements of results' reliability for structural/dynamical properties and related intermolecular interactions, and a mandatory principle of realism in the modeling strategy. Therefore, in practice, a truly realistic computational model of a biologically relevant system can easily fail to meet the accuracy requirement, in order to balance the excessive computational cost necessary to reach the desired precision.To address such an "accuracy vs reality" dualistic requirement, mixed quantum mechanics/classical mechanics approaches within Atomistic (i.e., preserving the discrete particle configuration) Polarizable Embeddings (QM/APEs) methods have been proposed over the years. In this Account, we review recent developments in the design and application of general QM/APE methods, targeting situations where a local intrinsically quantum behavior is coupled to a large molecular system (i.e., an environment), often involving processes with different dynamical time scales, in order to avoid brute-force, unpractical quantum chemistry calculations on the complete system.In the first place, our interest is devoted to the available APEs models presently implemented in computational software, highlighting the quantum chemistry methods that can be used to treat the QM subsystem. We review the coupling strategy between the QM subsystem and the APE, which requires to examine the way the QM/MM mutual interactions are accounted for and how the polarization of the classical environment is considered with respect to (wrt) the quantum variables. Because of the need of reliable molecular and macromolecular structures, a pivotal aspect to address here is the handling of the system dynamics (i.e., gradients wrt nuclear positions are required), especially for large molecular assemblies composed by an overwhelming number of atoms, exploring many conformations on a complex energy landscape.Alongside, we highlight our views on the necessary steps to take toward more accurate general-purposes and transferable explicit embeddings. The main objective to achieve here is to design a more physically grounded multiscale approach. To do so, one should apply advanced new generation classical models to account for refined induction effects that are able to (i) improve the quality of QM/MM interaction energies; (ii) enhance transferability by avoiding the compulsory partial (or total) reparameterization of the classical model. Moreover, the extension of recent developments originating from the field of advanced classical molecular dynamics (MD) to the realm of QM/APE methods is a key direction to improve both speed and efficiency for the phase space exploration of systems of growing size and complexity.Lastly, we point out specific research topics where an advanced QM/APE dynamics can certainly shed some light. For example, we discuss chemical reactions in "harsh" environments and the case of spectroscopic theoretical modeling where the inclusion of refined environment effects is often mandatory.
Collapse
Affiliation(s)
- Daniele Loco
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, 75005 Paris, France
| | - Louis Lagardère
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, 75005 Paris, France
- Intitut
Parisien de Chimie Physique et Théorique, Sorbonne Université, FR 2622 CNRS, 75005 Paris, France
| | - Olivier Adjoua
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, 75005 Paris, France
| | - Jean-Philip Piquemal
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, 75005 Paris, France
- Institut
Universitaire de France, F-75005 Paris, France
- Department
of Biomedical Engineering, The University
of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
8
|
Schieschke N, Bodenstein T, Höfener S. A Fock-operator complete active space self-consistent field (CAS-SCF) method combined with frozen-density embedding. J Chem Phys 2021; 154:084120. [PMID: 33639751 DOI: 10.1063/5.0037088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report the implementation of a Fock-operator complete-active space self-consistent field (CAS-SCF) method combined with frozen-density embedding (FDE) into the KOALA quantum-chemistry program. The implementation is based on configuration interaction from an unrestricted reference determinant and is able to treat electronic configurations such as singlet, triplet, or quintet states embedded in a molecular environment. In order to account for possible spin polarization effects, the FDE contribution is extended to the unrestricted case. We assess the convergence obtained with the implementation at the example of a stretched lithium dimer with significant multi-reference character. The efficiency of the implementation enables the orbital optimization for 25 states in a state-average SA[S0-S10,T1-T12,Q1-Q2]-CAS(10,10)-SCF calculation for the retinal molecule using a def2-TZVP basis. The FDE ansatz leads to orbitals localized by definition on the target system, thus facilitating the orbital selection required for CAS methods in complex environments.
Collapse
Affiliation(s)
- Nils Schieschke
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Tilmann Bodenstein
- Department of Chemistry, University of Oslo, Postboks 1033, Blindern, 0315 Oslo, Norway
| | - Sebastian Höfener
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| |
Collapse
|
9
|
Olsen JMH, Reine S, Vahtras O, Kjellgren E, Reinholdt P, Hjorth Dundas KO, Li X, Cukras J, Ringholm M, Hedegård ED, Di Remigio R, List NH, Faber R, Cabral Tenorio BN, Bast R, Pedersen TB, Rinkevicius Z, Sauer SPA, Mikkelsen KV, Kongsted J, Coriani S, Ruud K, Helgaker T, Jensen HJA, Norman P. Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems. J Chem Phys 2020; 152:214115. [PMID: 32505165 DOI: 10.1063/1.5144298] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The Dalton Project provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to the platform and made accessible to the user in the form of NumPy arrays, and the resulting data are extracted, analyzed, and visualized. Complex computational protocols that may, for instance, arise due to a need for environment fragmentation and configuration-space sampling of biochemical systems are readily assisted by the platform. The platform is designed to host additional software libraries and will serve as a hub for future modular software development efforts in the distributed Dalton community.
Collapse
Affiliation(s)
- Jógvan Magnus Haugaard Olsen
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Simen Reine
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, N-0315 Oslo, Norway
| | - Olav Vahtras
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Erik Kjellgren
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Karen Oda Hjorth Dundas
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Xin Li
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Janusz Cukras
- Department of Chemistry, University of Warsaw, 02-093 Warsaw, Poland
| | - Magnus Ringholm
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Erik D Hedegård
- Division of Theoretical Chemistry, Lund University, SE-223 62 Lund, Sweden
| | - Roberto Di Remigio
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Nanna H List
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Rasmus Faber
- DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | | | - Radovan Bast
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Thomas Bondo Pedersen
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, N-0315 Oslo, Norway
| | - Zilvinas Rinkevicius
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Kurt V Mikkelsen
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Kenneth Ruud
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Trygve Helgaker
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, N-0315 Oslo, Norway
| | - Hans Jørgen Aa Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Patrick Norman
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| |
Collapse
|
10
|
Marefat Khah A, Reinholdt P, Olsen JMH, Kongsted J, Hättig C. Avoiding Electron Spill-Out in QM/MM Calculations on Excited States with Simple Pseudopotentials. J Chem Theory Comput 2020; 16:1373-1381. [PMID: 32031806 DOI: 10.1021/acs.jctc.9b01162] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
QM/MM calculations of electronic excitations with diffuse basis sets often have large errors due to spill-out of electrons from the quantum subsystem. The Pauli repulsion of the electrons by the environment has to be included to avoid this. We propose transferable atomic all-electron pseudopotentials that can readily be combined with most MM force fields to avoid electron spill-out. QM/MM excitation energies computed with time-dependent Hartree-Fock and the algebraic diagrammatic construction through second-order are benchmarked against supermolecular calculations to validate these new pseudopotentials. The QM/MM calculations with pseudopotentials give accurate results that are stable with augmentation of the basis set with diffuse functions. We show that the largest contribution to residual deviations from full QM calculations is caused by the missing London dispersion interaction.
Collapse
Affiliation(s)
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT 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
| | - Christof Hättig
- Quantum Chemistry Group, Ruhr University of Bochum, D-44801 Bochum, Germany
| |
Collapse
|
11
|
Chen WK, Fang WH, Cui G. Integrating Machine Learning with the Multilayer Energy-Based Fragment Method for Excited States of Large Systems. J Phys Chem Lett 2019; 10:7836-7841. [PMID: 31786927 DOI: 10.1021/acs.jpclett.9b03113] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In this work we have combined machine learning techniques with our recently developed multilayer energy-based fragment method for studying excited states of large systems. The photochemically active and inert regions are separately treated with the complete active space self-consistent field method and the trained models. This method is demonstrated to provide accurate energies and gradients leading to essentially the same excited-state potential energy surfaces and nonadiabatic dynamics compared with full ab initio results. Furthermore, in conjunction with the use of machine learning models, this method is highly parallel and exhibits low-scaling computational cost. Finally, the present work could encourage the marriage of machine learning with fragment-based electronic structure methods to explore photochemistry of large systems.
Collapse
Affiliation(s)
- Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , People's Republic of China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , People's Republic of China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , People's Republic of China
| |
Collapse
|
12
|
Scheurer M, Reinholdt P, Kjellgren ER, Haugaard Olsen JM, Dreuw A, Kongsted J. CPPE: An Open-Source C++ and Python Library for Polarizable Embedding. J Chem Theory Comput 2019; 15:6154-6163. [PMID: 31580670 DOI: 10.1021/acs.jctc.9b00758] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We present a modular open-source library for polarizable embedding (PE) named CPPE. The library is implemented in C++, and it additionally provides a Python interface for rapid prototyping and experimentation in a high-level scripting language. Our library integrates seamlessly with existing quantum chemical program packages through an intuitive and minimal interface. Until now, CPPE has been interfaced to three packages, Q-Chem, Psi4, and PySCF. Furthermore, we show CPPE in action using all three program packages for a computational spectroscopy application. With CPPE, host program interfaces only require minor programming effort, paving the way for new combined methodologies and broader availability of the PE model.
Collapse
Affiliation(s)
- Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing , Heidelberg University , D-69120 Heidelberg , Germany.,Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Erik Rosendahl Kjellgren
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Jógvan Magnus Haugaard Olsen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry , UiT the Arctic University of Norway , N-9037 Tromsø , Norway
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing , Heidelberg University , D-69120 Heidelberg , Germany
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| |
Collapse
|
13
|
Schieschke N, Bodenstein T, Höfener S. Frozen-density embedding employing configuration interaction as a subsystem method. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1665726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Nils Schieschke
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | | | - Sebastian Höfener
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| |
Collapse
|
14
|
Liu H, Jenkins AJ, Wildman A, Frisch MJ, Lipparini F, Mennucci B, Li X. Time-Dependent Complete Active Space Embedded in a Polarizable Force Field. J Chem Theory Comput 2019; 15:1633-1641. [DOI: 10.1021/acs.jctc.8b01152] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Hongbin Liu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Andrew J. Jenkins
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Andrew Wildman
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Michael J. Frisch
- Gaussian Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
15
|
Marefat Khah A, Karbalaei Khani S, Hättig C. Analytic Excited State Gradients for the QM/MM Polarizable Embedded Second-Order Algebraic Diagrammatic Construction for the Polarization Propagator PE-ADC(2). J Chem Theory Comput 2018; 14:4640-4650. [PMID: 30040882 DOI: 10.1021/acs.jctc.8b00396] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
An implementation of a QM/MM embedding in a polarizable environment is presented for second-order Møller-Plesset perturbation theory, MP2, for ground state energies and molecular gradients and for the second-order Algebraic Diagrammatic Construction, ADC(2), for excitation energies and excited state molecular gradients. In this implementation of PE-MP2 and PE-ADC(2), the polarizable embedded Hartree-Fock wave function is used as uncorrelated reference state. The polarization-correlation cross terms for the ground and excited states are included in this model via an approximate coupling density. A Lagrangian formulation is used to derive the relaxed electron densities and molecular gradients. The resolution-of-the-identity approximation speeds up the calculation of four-index electron repulsion integrals in the molecular orbital basis. As a first application, the method is used to study the photophysical properties of host-guest complexes where the accuracy and weaknesses of the model are also critically examined. It is demonstrated that the ground state geometries of the full quantum mechanical calculation for the supermolecule can be well reproduced. For excited state geometries, the deviations from the supermolecular calculation are slightly larger, but still the environment effects are captured qualitatively correctly, and energy gaps between the ground and excited states are obtained with sufficient accuracy.
Collapse
Affiliation(s)
- Alireza Marefat Khah
- Arbeitsgruppe Quantenchemie , Ruhr-Universität Bochum , Bochum D-44801 , Germany
| | | | - Christof Hättig
- Arbeitsgruppe Quantenchemie , Ruhr-Universität Bochum , Bochum D-44801 , Germany
| |
Collapse
|
16
|
Hršak D, Olsen JMH, Kongsted J. Polarizable Density Embedding Coupled Cluster Method. J Chem Theory Comput 2018; 14:1351-1360. [DOI: 10.1021/acs.jctc.7b01153] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Dalibor Hršak
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jógvan Magnus Haugaard Olsen
- 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
| |
Collapse
|
17
|
Dong G, Ryde U, Aa. Jensen HJ, Hedegård ED. Exploration of H2 binding to the [NiFe]-hydrogenase active site with multiconfigurational density functional theory. Phys Chem Chem Phys 2018; 20:794-801. [DOI: 10.1039/c7cp06767d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The combination of density functional theory (DFT) with a multiconfigurational wave function is an efficient way to include dynamical correlation in calculations with multiconfiguration self-consistent field wave functions.
Collapse
Affiliation(s)
- Geng Dong
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
| | - Hans Jørgen Aa. Jensen
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- DK-5230 Odense M
- Denmark
| | - Erik D. Hedegård
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
| |
Collapse
|
18
|
Nørby MS, Olsen JMH, Steinmann C, Kongsted J. Modeling Electronic Circular Dichroism within the Polarizable Embedding Approach. J Chem Theory Comput 2017; 13:4442-4451. [DOI: 10.1021/acs.jctc.7b00712] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Morten S. Nørby
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | | | - Casper Steinmann
- Department
of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| |
Collapse
|
19
|
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
| |
Collapse
|
20
|
Hedegård ED, Bast R, Kongsted J, Olsen JMH, Jensen HJA. Relativistic Polarizable Embedding. J Chem Theory Comput 2017; 13:2870-2880. [DOI: 10.1021/acs.jctc.7b00162] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | - Radovan Bast
- High
Performance Computing Group, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | | | - Hans Jørgen Aagaard Jensen
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| |
Collapse
|
21
|
Saue T, Fromager E. Foreword for the special issue of Molecular Physics in honour of Hans Jørgen Aagaard Jensen. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1259259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Trond Saue
- Laboratoire de Chimie et Physique Quantiques, UMR 5626 CNRS, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Emmanuel Fromager
- Laboratoire de Chimie Quantique, Institut de Chimie, CNRS/Université de Strasbourg, Strasbourg, France
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
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
| |
Collapse
|
24
|
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
| |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
List NH, Jensen HJA, Kongsted J. Local electric fields and molecular properties in heterogeneous environments through polarizable embedding. Phys Chem Chem Phys 2016; 18:10070-80. [PMID: 27007060 DOI: 10.1039/c6cp00669h] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In spectroscopies, the local field experienced by a molecule embedded in an environment will be different from the externally applied electromagnetic field, and this difference may significantly alter the response and transition properties of the molecule. The polarizable embedding (PE) model has previously been developed to model the local field contribution stemming from the direct molecule-environment coupling of the electromagnetic response properties of molecules in solution as well as in heterogeneous environments, such as proteins. Here we present an extension of this approach to address the additional effective external field effect, i.e., the manifestations of the environment polarization induced by the external field, which allows for the calculation of properties defined in terms of the external field. Within a response framework, we report calculations of the one- and two-photon absorption (1PA and 2PA, respectively) properties of PRODAN-methanol clusters as well as the fluorescent protein DsRed. Our results demonstrate the necessity of accounting for both the dynamical reaction field and effective external field contributions to the local field in order to reproduce full quantum chemical reference calculations. For the lowest π→π* transition in DsRed, inclusion of effective external field effects gives rise to a 1.9- and 3.5-fold reduction in the 1PA and 2PA cross-sections, respectively. The effective external field is, however, strongly influenced by the heterogeneity of the protein matrix, and the resulting effect can lead to either screening or enhancement depending on the nature of the transition under consideration.
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
Sjulstok E, Olsen JMH, Solov'yov IA. Quantifying electron transfer reactions in biological systems: what interactions play the major role? Sci Rep 2015; 5:18446. [PMID: 26689792 PMCID: PMC4686879 DOI: 10.1038/srep18446] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/18/2015] [Indexed: 12/20/2022] Open
Abstract
Various biological processes involve the conversion of energy into forms that are usable for chemical transformations and are quantum mechanical in nature. Such processes involve light absorption, excited electronic states formation, excitation energy transfer, electrons and protons tunnelling which for example occur in photosynthesis, cellular respiration, DNA repair, and possibly magnetic field sensing. Quantum biology uses computation to model biological interactions in light of quantum mechanical effects and has primarily developed over the past decade as a result of convergence between quantum physics and biology. In this paper we consider electron transfer in biological processes, from a theoretical view-point; namely in terms of quantum mechanical and semi-classical models. We systematically characterize the interactions between the moving electron and its biological environment to deduce the driving force for the electron transfer reaction and to establish those interactions that play the major role in propelling the electron. The suggested approach is seen as a general recipe to treat electron transfer events in biological systems computationally, and we utilize it to describe specifically the electron transfer reactions in Arabidopsis thaliana cryptochrome-a signaling photoreceptor protein that became attractive recently due to its possible function as a biological magnetoreceptor.
Collapse
Affiliation(s)
- Emil Sjulstok
- 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
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| |
Collapse
|
29
|
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.
Collapse
Affiliation(s)
- Tobias Schwabe
- Center for Bioinformatics and Physical Chemistry Institute, University of Hamburg, Bundesstraße 43, D-20146 Hamburg, Germany
| |
Collapse
|
30
|
Hršak D, Marefat Khah A, Christiansen O, Hättig C. Polarizable Embedded RI-CC2 Method for Two-Photon Absorption Calculations. J Chem Theory Comput 2015; 11:3669-78. [PMID: 26574450 DOI: 10.1021/acs.jctc.5b00496] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We present a novel polarizable embedded resolution-of-identity coupled cluster singles and approximate doubles (PERI-CC2) method for calculation of two-photon absorption (TPA) spectra of large molecular systems. The method was benchmarked for three types of systems: a water-solvated molecule of formamide, a uracil molecule in aqueous solution, and a set of mutants of the channelrhodopsin (ChR) protein. The first test case shows that the PERI-CC2 method is in excellent agreement with the PE-CC2 method and in good agreement with the PE-CCSD method. The uracil test case indicates that the effects of hydrogen bonding on the TPA of a chromophore with the nearest environment is well-described with the PERI-CC2 method. Finally, the ChR calculation shows that the PERI-CC2 method is well-suited and efficient for calculations on proteins with medium-sized chromophores.
Collapse
Affiliation(s)
- Dalibor Hršak
- Center for Oxygen Microscopy and Imaging, Aarhus University , Langelandsgade 140, 8000 Aarhus, Denmark
| | - Alireza Marefat Khah
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum , Universitätsstraße 150, 44801 Bochum, Germany
| | - Ove Christiansen
- Center for Oxygen Microscopy and Imaging, Aarhus University , Langelandsgade 140, 8000 Aarhus, Denmark
| | - Christof Hättig
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum , Universitätsstraße 150, 44801 Bochum, Germany
| |
Collapse
|
31
|
Hedegård ED, Knecht S, Kielberg JS, Jensen HJA, Reiher M. Density matrix renormalization group with efficient dynamical electron correlation through range separation. J Chem Phys 2015; 142:224108. [DOI: 10.1063/1.4922295] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Erik Donovan Hedegård
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Stefan Knecht
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Jesper Skau Kielberg
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense, Denmark
| | - Hans Jørgen Aagaard Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense, Denmark
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| |
Collapse
|
32
|
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
| |
Collapse
|
33
|
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
| |
Collapse
|
34
|
Li Q, Mennucci B, Robb MA, Blancafort L, Curutchet C. Polarizable QM/MM Multiconfiguration Self-Consistent Field Approach with State-Specific Corrections: Environment Effects on Cytosine Absorption Spectrum. J Chem Theory Comput 2015; 11:1674-82. [DOI: 10.1021/ct5010388] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Quansong Li
- School
of Chemistry, Beijing Institute of Technology, Beijing 100081, China
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi, 56124 Pisa, Italy
| | - Michael A. Robb
- Department
of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
| | - Lluís Blancafort
- Institut
de Química Computacional i Catàlisi and Departament
de Química, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain
| | - Carles Curutchet
- Departament
de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
| |
Collapse
|
35
|
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
| |
Collapse
|
36
|
Harczuk I, Vahtras O, Ågren H. Frequency-dependent force fields for QMMM calculations. Phys Chem Chem Phys 2015; 17:7800-12. [DOI: 10.1039/c4cp05411c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The frequency-dependent localized polarizabilities are calculated for the first time using analytical response theory and benchmarked for different water clusters and the tryptophan residue embedded in a protein.
Collapse
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
| |
Collapse
|
37
|
Convergence of environment polarization effects in multiscale modeling of excitation energies. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.03.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
38
|
Pedersen MN, Hedegård ED, Olsen JMH, Kauczor J, Norman P, Kongsted J. Damped Response Theory in Combination with Polarizable Environments: The Polarizable Embedding Complex Polarization Propagator Method. J Chem Theory Comput 2014; 10:1164-71. [DOI: 10.1021/ct400946k] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Morten N. Pedersen
- 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
| | - Erik D. Hedegård
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jógvan Magnus H. Olsen
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Joanna Kauczor
- Department
of Physics, Chemistry and Biology, Linköping University, Linköping SE-58183, Sweden
| | - Patrick Norman
- Department
of Physics, Chemistry and Biology, Linköping University, Linköping SE-58183, Sweden
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| |
Collapse
|