Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems

Send, Robert; Kaila, Ville R. I.; Sundholm, Dage

doi:10.1063/1.3596729

Cited by 59 publications

(87 citation statements)

References 55 publications

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“…For both forms, CASPT2 gives the lowest excitation energies, QMC the highest ones, and CAM-B3LYP lies between the two, while NEVPT2, only employed on the B form, agrees reasonably well with QMC. Our findings are in line with other studies in literature on wild-type GFP 7,9,10,13 and other photosensitive biosystems 8,11,12,123 which found blue-shifted excitation energies compared to those of experiments using different quantum methods in combination with an MM environment. Including temperature effects, as done here and in previous work, 11,12,19 fails to improve on experimental agreement.…”

Section: Discussionsupporting

confidence: 95%

Chromophore–Protein Coupling beyond Nonpolarizable Models: Understanding Absorption in Green Fluorescent Protein

Daday

Curutchet

Sinicropi

et al. 2015

J. Chem. Theory Comput.

122

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The nature of the coupling of the photoexcited chromophore with the environment in a prototypical system like green fluorescent protein (GFP) is to date not understood, and its description still defies state-of-the-art multiscale approaches. To identify which theoretical framework of the chromophore-protein complex can realistically capture its essence, we employ here a variety of electronic-structure methods, namely, time-dependent density functional theory (TD-DFT), multireference perturbation theory (NEVPT2 and CASPT2), and quantum Monte Carlo (QMC) in combination with static point charges (QM/MM), DFT embedding (QM/DFT), and classical polarizable embedding through induced dipoles (QM/MMpol). Since structural modifications can significantly affect the photophysics of GFP, we also account for thermal fluctuations through extensive molecular dynamics simulations. We find that a treatment of the protein through static point charges leads to significantly blue-shifted excitation energies and that including thermal fluctuations does not cure the coarseness of the MM description. While TDDFT calculations on large cluster models indicate the need of a responsive protein, this response is not simply electrostatic: An improved description of the protein in the ground state or in response to the excitation of the chromophore via ground-state or state-specific DFT and MMpol embedding does not significantly modify the results obtained with static point charges. Through the use of QM/MMpol in a linear response formulation, a different picture in fact emerges in which the main environment response to the chromophore excitation is the one coupling the transition density and the corresponding induced dipoles. Such interaction leads to significant red-shifts and a satisfactory agreement with full QM cluster calculations at the same level of theory. Our findings demonstrate that, ultimately, faithfully capturing the effects of the environment in GFP requires a quantum treatment of large photoexcited regions but that a QM/classical model can be a useful approximation when extended beyond the electrostatic-only formulation.

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Section: Discussionsupporting

confidence: 95%

Chromophore–Protein Coupling beyond Nonpolarizable Models: Understanding Absorption in Green Fluorescent Protein

Daday

Curutchet

Sinicropi

et al. 2015

J. Chem. Theory Comput.

122

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“…polSS 1 e e 0 g g (14) The starting wave functions Ψ 0 (0) and Ψ 1 (0) are obtained in the presence of the static classical point charges, and at each iteration, the wave functions are optimized in a state-average (SA) fashion since the systems considered here have no symmetry. We note that while in the polGS excitation energy the solvent energy U solvent cancels out as already mentioned above, this is not the case in the polSS energy difference since two different sets of dipoles are employed.…”

Section: Methodsmentioning

confidence: 99%

Introducing QMC/MMpol: Quantum Monte Carlo in Polarizable Force Fields for Excited States

Guareschi

Zulfikri

Daday

et al. 2016

J. Chem. Theory Comput.

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We present for the first time a quantum mechanics/molecular mechanics scheme which combines quantum Monte Carlo with the reaction field of classical polarizable dipoles (QMC/MMpol). In our approach, the optimal dipoles are self-consistently generated at the variational Monte Carlo level and then used to include environmental effects in diffusion Monte Carlo. We investigate the performance of this hybrid model in describing the vertical excitation energies of prototypical small molecules solvated in water, namely, methylenecyclopropene and s-trans acrolein. Two polarization regimes are explored where either the dipoles are optimized with respect to the ground-state solute density (polGS) or different sets of dipoles are separately brought to equilibrium with the states involved in the electronic transition (polSS). By comparing with reference supermolecular calculations where both solute and solvent are treated quantum mechanically, we find that the inclusion of the response of the environment to the excitation of the solute leads to superior results than the use of a frozen environment (point charges or polGS), in particular, when the solute-solvent coupling is dominated by electrostatic effects which are well recovered in the polSS condition. QMC/MMpol represents therefore a robust scheme to treat important environmental effects beyond static point charges, combining the accuracy of QMC with the simplicity of a classical approach.

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“…Recently, the structure of the first light-activated Na + pump, Krokinobacter eikastus rhodopsin 2 (KR2), was resolved at atomic resolution [Kato HE, et al (2015) Nature 521: [48][49][50][51][52][53]. To elucidate its molecular mechanism for Na + pumping, we perform here extensive classical and quantum molecular dynamics (MD) simulations of transient photocycle states.…”

mentioning

confidence: 99%

Energetics and dynamics of a light-driven sodium-pumping rhodopsin

Suomivuori

Gámiz‐Hernández

Sundholm

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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The conversion of light energy into ion gradients across biological membranes is one of the most fundamental reactions in primary biological energy transduction. Recently, the structure of the first light-activated Na + pump, Krokinobacter eikastus rhodopsin 2 (KR2), was resolved at atomic resolution [Kato HE, et al. (2015) Nature 521: [48][49][50][51][52][53]. To elucidate its molecular mechanism for Na + pumping, we perform here extensive classical and quantum molecular dynamics (MD) simulations of transient photocycle states. Our simulations show how the dynamics of key residues regulate water and ion access between the bulk and the buried light-triggered retinal site. We identify putative Na + binding sites and show how protonation and conformational changes gate the ion through these sites toward the extracellular side. We further show by correlated ab initio quantum chemical calculations that the obtained putative photocycle intermediates are in close agreement with experimental transient optical spectroscopic data. The combined results of the ion translocation and gating mechanisms in KR2 may provide a basis for the rational design of novel light-driven ion pumps with optogenetic applications.bacterial ion pumps | bioenergetics | QM/MM | optogenetics | retinal P rimary biological energy conversion is based on the efficient capture and conversion of light and chemical energy into ion gradients across biological membranes (1, 2). The established gradients are used to thermodynamically drive energy-requiring processes, such as active transport and synthesis of adenosine triphosphate (ATP) (3, 4). The rhodopsin family of proteins catalyzes such reactions by harnessing the energy from retinal photoisomerization and deprotonation reactions, followed by conformational changes that further trigger the pumping of ions across the membrane (5). All previously known ion-pumping rhodopsins function either as inward chloride or outward proton pumps, but the structure of the first Na + pumping rhodopsin, Krokinobacter eikastus rhodopsin 2 (KR2) (6), was recently resolved (7,8). In the absence of Na + ions, KR2 functions as an outward proton pump, similarly to bacteriorhodopsin (bR), but under physiological conditions, KR2 pumps Na + out of the cell (6, 9).KR2 shares the heptahelical transmembrane (7TM) structure common to all microbial rhodopsins (Fig. 1A) (5,7,8). In contrast to bR, however, where a highly conserved Asp-Thr-Asp (DTD) motif is used to pump protons, KR2 employs a unique NDQ motif comprising residues Asn112, Asp116, and Gln123 (6). In bR, Asp85 and Asp96 function as proton acceptors and donors for the protonated Schiff base (PSB), respectively, whereas in KR2, Asn112 and Gln123 occupy these positions, and Asp116 replaces Thr89. In analogy to bR, it has been suggested that Gln123 aids in capturing ions from the solvent and that Asn112 might be part of a Na + binding site (6,10).Similarly to other microbial rhodopsins, four photocycle intermediates have been spectroscopically identified in KR2 (Fig. 1B) (6)...

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Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems

Cited by 59 publications

References 55 publications

Chromophore–Protein Coupling beyond Nonpolarizable Models: Understanding Absorption in Green Fluorescent Protein

Chromophore–Protein Coupling beyond Nonpolarizable Models: Understanding Absorption in Green Fluorescent Protein

Introducing QMC/MMpol: Quantum Monte Carlo in Polarizable Force Fields for Excited States

Energetics and dynamics of a light-driven sodium-pumping rhodopsin

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