Polarizable Density Embedding: A New QM/QM/MM-Based Computational Strategy

Olsen, Jógvan Magnus Haugaard; Steinmann, Casper; Ruud, Kenneth; Kongsted, Jacob

doi:10.1021/jp510138k

Cited by 89 publications

(166 citation statements)

References 87 publications

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“…In light of this, we here show the importance of utilizing an accurate embedding potential that is derived from first principles and which can reproduce the true quantum mechanical embedding potential and is not taken from a traditional protein force field. 32 Such a potential also accurately levels of theory. This is followed, in Section 3, by a brief discussion of the computational methodologies involved.…”

Section: Introductionmentioning

confidence: 92%

Electronic Energy Transfer in Polarizable Heterogeneous Environments: A Systematic Investigation of Different Quantum Chemical Approaches

Steinmann

Kongsted

2015

J. Chem. Theory Comput.

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Theoretical prediction of transport and optical properties of protein-pigment complexes is of significant importance when aiming at understanding the structure-function relationship in such systems. Electronic energy transfer (EET) couplings represent a key property in this respect since such couplings provide important insight into the strength of interaction between photoactive pigments in protein-pigment complexes. Recently, attention has been payed to how the environment modifies or even controls the electronic couplings. To enable such theoretical predictions, a fully polarizable embedding model has been suggested (Curutchet, C., et al. J. Chem. Theory Comput., 2009, 5, 1838-1848). In this work, we further develop this computational model by extending it with an ab initio derived polarizable force field including higher-order multipole moments. We use this extended model to systematically examine three different ways of obtaining EET couplings in a heterogeneous medium ranging from use of the exact transition density to a point-dipole approximation. Several interesting observations are made, for example, the explicit use of transition densities in the calculation of the electronic couplings, and also when including the explicit environment contribution, can be replaced by a much simpler transition point charge description without comprising the quality of the model predictions.

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Section: Introductionmentioning

confidence: 92%

Electronic Energy Transfer in Polarizable Heterogeneous Environments: A Systematic Investigation of Different Quantum Chemical Approaches

Steinmann

Kongsted

2015

J. Chem. Theory Comput.

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“…The effectiveness of these embedding methods will therefore depend on eliminating the need for iterative freeze-and-thaw cycles and/or increasing the number of basis functions truncated. Olsen and co-workers 38 have implemented a strategy that eliminates the need for mutual polarization through iterative freeze-and-thaw cycles by using a classical polarizable force field. Additionally, one may employ the dual truncation strategy of reducing the number of atoms in the overlap region as well as the quality of these overlap AOs when working with noncovalent systems or covalent systems with localized charge distributions.…”

Section: Effects Of Basis Set Truncationmentioning

confidence: 99%

Frozen Density Embedding with External Orthogonality in Delocalized Covalent Systems

Chulhai

Jensen

2015

J. Chem. Theory Comput.

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Frozen density embedding (FDE) has become a popular subsystem density functional theory (DFT) method for systems with weakly overlapping charge densities. The failure of this method for strongly interacting and covalent systems is due to the approximate kinetic energy density functional (KEDF), although the need for approximate KEDFs may be eliminated if each subsystem's Kohn-Sham (KS) orbitals are orthogonal to the other, termed external orthogonality (EO). We present an implementation of EO into the FDE framework within the Amsterdam density functional program package, using the level-shift projection operator method. We generalize this method to remove the need for orbital localization schemes and to include multiple subsystems, and we show that the exact KS-DFT energies and densities may be reproduced through iterative freeze-and-thaw cycles for a number of systems, including a charge delocalized benzene molecule starting from atomic subsystems. Finally, we examine the possibility of a truncated basis for systems with and without charge delocalization, and found that subsystems require a basis that allows them to correctly describe the supermolecular delocalized orbitals.

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“…[35][36][37][38] The description of electrostatics and polarization is nearly identical in EFP and PE; however, EFP features more rigorous treatment of dispersion and exchange-repulsion. For modeling intermolecular interactions, similar strategies based on multipolar expansion have been utilized.…”

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confidence: 99%

Extension of the Effective Fragment Potential Method to Macromolecules

et al. 2016

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The effective fragment potential (EFP) approach, which can be described as a nonempirical polarizable force field, affords an accurate first-principles treatment of noncovalent interactions in extended systems. EFP can also describe the effect of the environment on the electronic properties (e.g., electronic excitation energies and ionization and electron-attachment energies) of a subsystem via the QM/EFP (quantum mechanics/EFP) polarizable embedding scheme. The original formulation of the method assumes that the system can be separated, without breaking covalent bonds, into closed-shell fragments, such as solvent and solute molecules. Here, we present an extension of the EFP method to macromolecules (mEFP). Several schemes for breaking a large molecule into small fragments described by EFP are presented and benchmarked. We focus on the electronic properties of molecules embedded into a protein environment and consider ionization, electron-attachment, and excitation energies (single-point calculations only). The model systems include chromophores of green and red fluorescent proteins surrounded by several nearby amino acid residues and phenolate bound to the T4 lysozyme. All mEFP schemes show robust performance and accurately reproduce the reference full QM calculations. For further applications of mEFP, we recommend either the scheme in which the peptide is cut along the Cα-C bond, giving rise to one fragment per amino acid, or the scheme with two cuts per amino acid, along the Cα-C and Cα-N bonds. While using these fragmentation schemes, the errors in solvatochromic shifts in electronic energy differences (excitation, ionization, electron detachment, or electron-attachment) do not exceed 0.1 eV. The largest error of QM/mEFP against QM/EFP (no fragmentation of the EFP part) is 0.06 eV (in most cases, the errors are 0.01-0.02 eV). The errors in the QM/molecular mechanics calculations with standard point charges can be as large as 0.3 eV.

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Polarizable Density Embedding: A New QM/QM/MM-Based Computational Strategy

Cited by 89 publications

References 87 publications

Electronic Energy Transfer in Polarizable Heterogeneous Environments: A Systematic Investigation of Different Quantum Chemical Approaches

Electronic Energy Transfer in Polarizable Heterogeneous Environments: A Systematic Investigation of Different Quantum Chemical Approaches

Frozen Density Embedding with External Orthogonality in Delocalized Covalent Systems

Extension of the Effective Fragment Potential Method to Macromolecules

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