Infrared spectroscopy from electrostatic embedding QM/MM: local normal mode analysis of infrared spectra of arabidopsis thaliana plant cryptochrome

Huix‐Rotllant, Miquel; Schwinn, Karno; Ferré, Nicolas

doi:10.1039/d0cp06070d

Cited by 9 publications

(9 citation statements)

References 56 publications

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“…Energetics from electronic transitions (ground‐state S 0 → excited state S n ) that explains UV/Vis absorption (one‐photon and two‐photon absorption) and emission properties 34,80 Vibrational properties underlying infrared, Raman, and resonance Raman spectra 81–84 Electromagnetic properties such as NMR chemical shifts and EPR hyperfine structure 47,85,86 …”

Section: Methodsmentioning

confidence: 99%

Understanding flavin electronic structure and spectra

Kar

Miller

Mroginski

2021

WIREs Comput Mol Sci

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Flavins have emerged as central to electron bifurcation, signaling, and countless enzymatic reactions. In bifurcation, two electrons acquired as a pair are separated in coupled transfers wherein the energy of both is concentrated on one of the two. This enables organisms to drive demanding reactions based on abundant low‐grade chemical fuel. To enable incorporation of this and other flavin capabilities into designed materials and devices, it is essential to understand fundamental principles of flavin electronic structure that make flavins so reactive and tunable by interactions with protein. Emerging computational tools can now replicate spectra of flavins and are gaining capacity to explain reactivity at atomistic resolution, based on electronic structures. Such fundamental understanding can moreover be transferrable to other chemical systems. A variety of computational innovations have been critical in reproducing experimental properties of flavins including their electronic spectra, vibrational signatures, and nuclear magnetic resonance (NMR) chemical shifts. A computational toolbox for understanding flavin reactivity moreover must be able to treat all five oxidation and protonation states, in addition to excited states that participate in flavoprotein's light‐driven reactions. Therefore, we compare emerging hybrid strategies and their successes in replicating effects of hydrogen bonding, the surrounding dielectric, and local electrostatics. These contribute to the protein's ability to modulate flavin reactivity, so we conclude with a survey of methods for incorporating the effects of the protein residues explicitly, as well as local dynamics. Computation is poised to elucidate the factors that affect a bound flavin's ability to mediate stunningly diverse reactions, and make life possible. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Combined QM/MM Methods Theoretical and Physical Chemistry > Spectroscopy

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Section: Methodsmentioning

confidence: 99%

Understanding flavin electronic structure and spectra

Kar

Miller

Mroginski

2021

WIREs Comput Mol Sci

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“…To simulate condensed-phase FTIR spectra, computational models must account for the effect of intermolecular interactions on molecular vibrations. Understanding how to best model FTIR spectra in the condensed phase can be especially useful for developing suitable protocols to simulate FTIR spectra of biomolecules, where shifts in IR frequencies (often measured using difference spectroscopy) encode important information about changes in local interactions or macromolecular structure [ 2 , 3 , 4 ]. For instance, FTIR spectroscopies have been used to probe intermediates formed following the photoexcitation of several flavin-binding photoreceptors [ 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

“…For instance, FTIR spectroscopies have been used to probe intermediates formed following the photoexcitation of several flavin-binding photoreceptors [ 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 ]. FTIR spectra of protein-bound flavin have also been simulated using hybrid quantum mechanical/molecular mechanical (QM/MM) methods to accompany such experiments [ 4 , 18 , 19 , 20 , 21 , 22 ].…”

Section: Introductionmentioning

confidence: 99%

How Aqueous Solvation Impacts the Frequencies and Intensities of Infrared Absorption Bands in Flavin: The Quest for a Suitable Solvent Model

Le,

Hastings,

Gozem

2024

Molecules

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FTIR spectroscopy accompanied by quantum chemical simulations can reveal important information about molecular structure and intermolecular interactions in the condensed phase. Simulations typically account for the solvent either through cluster quantum mechanical (QM) models, polarizable continuum models (PCM), or hybrid quantum mechanical/molecular mechanical (QM/MM) models. Recently, we studied the effect of aqueous solvent interactions on the vibrational frequencies of lumiflavin, a minimal flavin model, using cluster QM and PCM models. Those models successfully reproduced the relative frequencies of four prominent stretching modes of flavin’s isoalloxazine ring in the diagnostic 1450–1750 cm−1 range but poorly reproduced the relative band intensities. Here, we extend our studies on this system and account for solvation through a series of increasingly sophisticated models. Only by combining elements of QM clusters, QM/MM, and PCM approaches do we obtain an improved agreement with the experiment. The study sheds light more generally on factors that can impact the computed frequencies and intensities of IR bands in solution.

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“…[54][55][56][57], including molecular systems in aqueous solution. [58][59][60][61] While the calculation of anharmonic vibrational energy levels is less established, most impor-tantly because it is associated with a higher computational effort, tremendous progress has been made in the past decades. [62][63][64][65][66][67][68][69][70] Most importantly, efficient approximate schemes for the inclusion of anharmonicities in theoretical vibrational spectroscopy have become available that are applicable to medium-seized molecules, including polypeptides.…”

Section: Introductionmentioning

confidence: 99%

Quantum-chemical calculation of two-dimensional infrared spectra using localized-mode VSCF/VCI

Brüggemann

Wolter

Jacob

2022

Preprint

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Computational protocols for the simulation of two-dimensional infrared (2D IR) spectroscopy usually rely on vibrational exciton models, which require an empirical parametrization. Here, we present an efficient quantum-chemical protocol for predicting static 2D IR spectra that does not require any empirical parameters. For the calculation of anharmonic vibrational energy levels and transition dipole moments, we employ the localized-mode vibrational self-consistent field (L-VSCF) / vibrational configuration interaction (L-VCI) approach previous established for (linear) anharmonic theoretical vibrational spectroscopy [Panek and Jacob, ChemPhysChem 15, 3365–3377 (2014)]. We demonstrate that with an efficient expansion of the potential energy surface using anharmonic one-mode potentials and harmonic two-mode potentials, 2D IR spectra of metal carbonyl complexes and of dipeptides can be predicted reliably. We further show how the close connection between L-VCI and vibrational exciton models can be exploited to extract the parameters of such models from those calculations. This provides a novel route to the fully quantum-chemical parametrization of vibrational exciton model for predicting 2D IR spectra.

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Infrared spectroscopy from electrostatic embedding QM/MM: local normal mode analysis of infrared spectra of arabidopsis thaliana plant cryptochrome

Abstract: Combined QM/MM Hessians and local normal mode analysis are powerful tools to simulate and interpret complex IR spectra of biological macromolecules.

Cited by 9 publications

References 56 publications

Understanding flavin electronic structure and spectra

Understanding flavin electronic structure and spectra

How Aqueous Solvation Impacts the Frequencies and Intensities of Infrared Absorption Bands in Flavin: The Quest for a Suitable Solvent Model

Quantum-chemical calculation of two-dimensional infrared spectra using localized-mode VSCF/VCI

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