Modeling Photobiology Using Quantum Mechanics and Quantum Mechanics/Molecular Mechanics Calculations

Li, Xin; Chung, Lung Wa; Morokuma, Keiji

doi:10.1002/9780470930779.ch12

Cited by 2 publications

(3 citation statements)

References 113 publications

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“…Inspired by previous studies, , two different gas-phase models, MS (32 atoms) without a CH 2 CH 2 OH group in the chromophore and thus without a hydrogen bond between CRO and Glu219 and ML (39 atoms) with CH 2 CH 2 OH and thus with a hydrogen bond (Scheme b), were constructed. The QM model including more H-bonds might help to provide more accurate results.…”

Section: Computational Detailsmentioning

confidence: 99%

“…In particular, it is a challenge to characterize the nature of the electronic structures involved and details of the decarboxylation process. Recently, our group theoretically investigated the reaction mechanisms of the reversible photoswitching process in Dronpa and the irreversible photoconversion in Kaede by the ONIOM(QM:MM) method and proposed new mechanisms, namely, photoisomerization coupled with ESPT in Donpa and E 1cb in Kaede . Intrigued by the still-unclear photodecarboxylation process, one important advantage of PA-GFP is amazing contrast enhancement (∼100-fold), compared to that in wt-GFP.…”

Section: Introductionmentioning

confidence: 99%

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Reaction Mechanism of Photoinduced Decarboxylation of the Photoactivatable Green Fluorescent Protein: An ONIOM(QM:MM) Study

2013

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Photoactivatable (PA) fluorescent proteins are a new class of fluorescent proteins in which the intensity of fluorescence is dramatically enhanced through photoinduced decarboxylation process. In the present study, the reaction mechanism of the photoinduced decarboxylation in PA-GFP was investigated by the ONIOM(QM:MM) method. The decarboxylation process starts from the first excited state (IntraCT state) and then proceeds along an InterCT state after the first crossing (or an approximate transition state). Relative to an equilibrium structure in S(0), a barrier of ~94 kcal/mol to reach this approximate transition state is the rate-determining step for the entire decarboxylation process. The InterCT state becomes the open-shell ground state in the product, after the subsequent crossing with a closed-shell state that holds an extra electron on the dissociated CO(2). The present study elucidated for the first time the mechanism of the photoinduced decarboxylation of PA-GFP and supports the widely accepted Kolbe pathway, which could be a common mechanism for the irreversible photoinduced decarboxylation in different fluorescent proteins.

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Section: Computational Detailsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Reaction Mechanism of Photoinduced Decarboxylation of the Photoactivatable Green Fluorescent Protein: An ONIOM(QM:MM) Study

2013

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“…Therefore, in systems significantly larger than 100 atoms, but not large enough that rigorous linear scaling is possible, it is necessary to apply additional approximations . Exploiting the intrinsic locality in certain types of chromophores has led to the development of incremental, multilayer, and fragmentation-based approaches. − Biological systems often fall into this category, and reports of heroic calculations with over 20 000 atoms have been reported . However, the excited states for these systems were only computed on fragments containing no more than 103 atoms.…”

Section: Introductionmentioning

confidence: 99%

Superposition of Fragment Excitations for Excited States of Large Clusters with Application to Helium Clusters

Closser

Mao

et al. 2015

J. Chem. Theory Comput.

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We develop a local excited-state method, based on the configuration interaction singles (CIS) wave function, for large atomic and molecular clusters. This method exploits the properties of absolutely localized molecular orbitals (ALMOs), which strictly limits the total number of excitations, and results in formal scaling with the third power of the system size for computing the full spectrum of ALMO-CIS excited states. The derivation of the equations and design of the algorithm are discussed in detail, with particular emphasis on the computational scaling. Clusters containing ∼500 atoms were used in evaluating the scaling, which agrees with the theoretical predictions, and the accuracy of the method is evaluated with respect to standard CIS. A pioneering application to the size dependence of the helium cluster spectrum is also presented for clusters of 25-231 atoms, the largest of which results in the computation of 2310 excited states per sampled cluster geometry.

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Modeling Photobiology Using Quantum Mechanics and Quantum Mechanics/Molecular Mechanics Calculations

Cited by 2 publications

References 113 publications

Reaction Mechanism of Photoinduced Decarboxylation of the Photoactivatable Green Fluorescent Protein: An ONIOM(QM:MM) Study

Reaction Mechanism of Photoinduced Decarboxylation of the Photoactivatable Green Fluorescent Protein: An ONIOM(QM:MM) Study

Superposition of Fragment Excitations for Excited States of Large Clusters with Application to Helium Clusters

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