Three-Layer ONIOM Studies of the Dark State of Rhodopsin: The Protonation State of Glu181

Hall, Katherine F.; Vreven, Thorn; Frisch, Michael J.; Bearpark, Michael J.

doi:10.1016/j.jmb.2008.08.007

Cited by 40 publications

(51 citation statements)

References 72 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Some of us showed that as long as there is a core part, ONIOM can even partition the chromophore into different regions. 18,22 Whereas the behavior of ONIOM for ground state energies has been investigated in numerous works, there are only few reports in the literature on the calculation of transition energies, [22][23][24][25][26][27][28][29][30][31][32][33][34] of which several used QM/QM combinations. The goal of this work is to investigate further the effectiveness of ONIOM͑QM:QM͒ for the description of excited states.…”

Section: Introductionmentioning

confidence: 99%

Using the ONIOM hybrid method to apply equation of motion CCSD to larger systems: Benchmarking and comparison with time-dependent density functional theory, configuration interaction singles, and time-dependent Hartree–Fock

Caricato

Vreven

Trucks

et al. 2009

The Journal of Chemical Physics

Self Cite

View full text Add to dashboard Cite

Assessment of time-dependent density functional schemes for computing the oscillator strengths of benzene, phenol, aniline, and fluorobenzene J. Chem. Phys. 127, 084103 (2007) Equation of motion coupled-cluster singles and doubles ͑EOM-CCSD͒ is one of the most accurate computational methods for the description of one-electron vertical transitions. However, its O͑N 6 ͒ scaling, where N is the number of basis functions, often makes the study of molecules larger than 10-15 heavy atoms prohibitive. In this work we investigate how accurately less expensive methods can approximate the EOM-CCSD results. We focus on our own N-layer integrated molecular orbital molecular mechanics ͑ONIOM͒ hybrid scheme, where the system is partitioned into regions which are treated with different levels of theory. For our set of benchmark calculations, the comparison of conventional configuration interaction singles ͑CIS͒, time-dependent Hartree-Fock ͑TDHF͒, and time-dependent density functional theory ͑TDDFT͒ methods and ONIOM ͑with different low level methods͒ showed that the best accuracy-computational time combination is obtained with ONIOM͑EOM:TDDFT͒, which has a rms of the error with respect to the conventional EOM-CCSD of 0.06 eV, compared with 0.47 eV of the conventional TDDFT.

show abstract

Section: Introductionmentioning

confidence: 99%

Using the ONIOM hybrid method to apply equation of motion CCSD to larger systems: Benchmarking and comparison with time-dependent density functional theory, configuration interaction singles, and time-dependent Hartree–Fock

Caricato

Vreven

Trucks

et al. 2009

The Journal of Chemical Physics

Self Cite

View full text Add to dashboard Cite

show abstract

“…In the simplest two-layer case, it corresponds to a standard QM/MM approach, whereas more advanced options are also in use, such as QM/QM approaches like CASSCF/Hartree-Fock (HF) [102] or three-layer DFT/ HF/MM schemes. [19] In a three-layer scheme, there is a "model region" corresponding to the active part that should be described with high accuracy, an "intermediate region" surrounding the active part, and an environmental region. In the ONIOM nomenclature, the combination of the three regions is called the "real system".…”

Section: Qm/mm Models For Spectroscopic Propertiesmentioning

confidence: 99%

“…It goes without saying that subsystem-based theoretical approaches are very important in other types of spectroscopy, such as vibrational spectroscopy, where computational techniques like partial Hessian diagonalization, [6] mobile block Hessian approaches, [7,8] mode tracking/intensity tracking, [9][10][11][12][13][14][15] Cartesian tensor transfer techniques, [16] or normal-mode localization schemes [17] are employed. Other examples can be found in nuclear magnetic resonance spectroscopy, [18,19] electron spin resonance, [20,21] and Mçßbauer spectroscopy [21] (also see ref. [22]).…”

Section: Introductionmentioning

confidence: 99%

Subsystem‐Based Theoretical Spectroscopy of Biomolecules and Biomolecular Assemblies

Neugebauer

2009

ChemPhysChem

123

View full text Add to dashboard Cite

The absorption properties of chromophores in biomolecular systems are subject to several fine-tuning mechanisms. Specific interactions with the surrounding protein environment often lead to significant changes in the excitation energies, but bulk dielectric effects can also play an important role. Moreover, strong excitonic interactions can occur in systems with several chromophores at close distances. For interpretation purposes, it is often desirable to distinguish different types of environmental effects, such as geometrical, electrostatic, polarization, and response (or differential polarization) effects. Methods that can be applied for theoretical analyses of such effects are reviewed herein, ranging from continuum and point-charge models to explicit quantum chemical subsystem methods for environmental effects. Connections to physical model theories are also outlined. Prototypical applications to optical spectra and excited states of fluorescent proteins, biomolecular photoreceptors, and photosynthetic protein complexes are discussed.

show abstract

“…In case of severed bonds at the boundary between the model system and the rest, hydrogen link atoms are usually added for capping. The ONIOM extrapolation can be also formulated for vertical transition energies [19][20][21][22][23][24][25][26][27][28][29][30][31] with QM or MM methods as low level. One of us benchmarked ONIOM(QM:QM) for electronic transition energies and properties against a high level of theory such as the equation of motion coupled cluster singles and doubles (EOM-CCSD) method.…”

Section: Introductionmentioning

confidence: 99%

Point charge embedding for ONIOM excited states calculations

Biancardi

Barnes

Caricato

2016

The Journal of Chemical Physics

View full text Add to dashboard Cite

Hybrid quantum mechanical methods can assist in the interpretation and prediction of the electronic spectra of large molecular structures. In this work, we study the performance of the ONIOM (Our own N-layered Integrated molecular Orbital molecular Mechanics) hybrid method for the calculation of transition energies and oscillator strengths by embedding the core region in a field of fixed point charges. These charges introduce polarization effects from the substituent groups to the core region. We test various charge definitions, with particular attention to the issue of overpolarization near the boundary between layers. To minimize this issue, we fit the charges on the electrostatic potential of the entire structure in the presence of the link atoms used to cap dangling bonds. We propose two constrained fitting strategies: one that produces an average set of charges common to both model system calculations, EE(L1), and one that produces two separate sets of embedding charges, EE(L2). The results from our tests show that indeed electronic embedding with constrained-fitted charges tends to improve the performance of ONIOM compared to non-embedded calculations. However, the EE(L2) charges work best for transition energies, and the EE(L1) charges work best for oscillator strengths. This may be an indication that fixed point charges do not have enough flexibility to adapt to each system, and other effects (e.g., polarization of the embedding field) may be necessary. Published by AIP Publishing. [http://dx

show abstract

Three-Layer ONIOM Studies of the Dark State of Rhodopsin: The Protonation State of Glu181

Cited by 40 publications

References 72 publications

Using the ONIOM hybrid method to apply equation of motion CCSD to larger systems: Benchmarking and comparison with time-dependent density functional theory, configuration interaction singles, and time-dependent Hartree–Fock

Using the ONIOM hybrid method to apply equation of motion CCSD to larger systems: Benchmarking and comparison with time-dependent density functional theory, configuration interaction singles, and time-dependent Hartree–Fock

Subsystem‐Based Theoretical Spectroscopy of Biomolecules and Biomolecular Assemblies

Point charge embedding for ONIOM excited states calculations

Contact Info

Product

Resources

About