Discovery of conical intersection mediated photochemistry with growing string methods

Aldaz, Cody R.; Kammeraad, Joshua; Zimmerman, Paul M.

doi:10.1039/c8cp04703k

Cited by 34 publications

(45 citation statements)

References 85 publications

(92 reference statements)

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“…In Refinement, minimum energy paths connecting pairs of MECIs on the seam space and stationary points on the ground state are computed using the growing string method (GSM). 27,56 This allows us to identify barriers within the seam and make hypotheses on the accessibility of a given CI type.…”

Section: Theory and Methodsmentioning

confidence: 99%

“…All the electronic structure calculations used in this work are performed using the TeraChem [58][59][60] software package and pyGSM 27 is used for optimization of minimum energy paths. The use of GPU-accelerated code makes the global computational effort very affordable.…”

Section: Theory and Methodsmentioning

confidence: 99%

“…For example, Aldaz et al used combinatorically generated reaction coordinates to search for MECIs and then followed the ground-state down to photoproducts. 27 Others have developed tools for the systematic exploration of the intersection seam using modified potential energy surfaces and molecular dynamics. For example, Maeda et al 28 combined the seam model function with multicomponent artificial force induced reaction (SMF/MC-AFIR) to automatically identify and characterize large numbers of available CIs.…”

Section: Introductionmentioning

confidence: 99%

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The non-adiabatic nanoreactor: towards the automated discovery of photochemistry

et al. 2021

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Section: Theory and Methodsmentioning

confidence: 99%

Section: Theory and Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The non-adiabatic nanoreactor: towards the automated discovery of photochemistry

et al. 2021

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“…39 The procedure used for fitting the a-parameter and its validation against extended multistate multireference secondorder perturbation theory (XMS-CASPT2 48 ) is described in Section S1 of the supplementary information (SI). Geometry optimization, minimum conical intersection (MECI) searches and minimum energy pathways (MEPs) were computed using the DL-FIND 49 geometry optimization library and seam MEPs using pyGSM, [50][51] both interfaced with TeraChem. XMS-CASPT2 calculations were performed using the BAGEL program.…”

Section: Computational Detailsmentioning

confidence: 99%

Internal Conversion of the Anionic GFP Chromophore: In and Out of the I-twisted S1/S0 Conical Intersection Seam

List

Jones²,

Martı́nez³

2021

Preprint

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The functional diversity of the green fluorescent protein (GFP) family is intimately connected to the interplay between competing photo-induced transformations of the chromophore motif, anionic p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI–). Its propensity to undergo Z/E photoisomerization following excitation to the S1(pp*) state is of particular importance for super-resolution microscopy and emerging opportunities in optogenetics. However, key dynamical aspects of this process and its range of tunability still remain elusive. Here, we investigate the internal conversion behavior intrinsic to HBDI– with focus on competing deactivation pathways, rate and yield of photoisomerization. Based on non-adiabatic dynamics simulations, we confirm that non-selective progress along the two bridge-torsional (i.e., phenolate, P, or imidazolinone, I) pathways can account for the three decay constants reported experimentally, leading to competing ultrafast relaxation along the I-twisted pathway and S1 trapping along the P-torsion. The majority of the population (~70%) is transferred to S0 in the vicinity of two near-symmetry-related minima on the I-twisted intersection seam (MECI-Is). Despite their reactant-biased topographies, our account of inertial effects suggests that isomerization not only occurs as a thermal process on the vibrationally hot ground state but also as a direct photoreaction with a total quantum yield of ~40%.By comparing the non-adiabatic dynamics to a photoisomerization committor analysis, we provide a detailed mapping of the intrinsic photoreactivity and dynamical behavior of the two MECI-Is. Our work offers new insight into the internal conversion process of HBDI– that enlightens principles for the design of chromophore derivatives and protein variants with improved photoswitching properties.

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“…The difference in photoproducts is the orientation of the resulting . This is unusual because rotation of hydrogen out of plane has only been found in the gas-phase as a high-energy seam saddle point 23,42,55 .…”

Section: Obf Double Bond Rotationmentioning

confidence: 99%

The Mechanics of the Bicycle Pedal Photoisomerization in Crystalline cis,cis-1,4-Diphenyl-1,3-butadiene

2020

Self Cite

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Direct irradiation of crystalline cis,cis-1,4-diphenyl-1,3-butadiene (cc-DPB) forms trans,trans-1,4-diphenyl-1,3,-butadiene via a concerted two bond isomerization called the bicycle pedal mechanism. However, little is known about photoisomerization pathways in the solid-state and there has been much debate surrounding the interpretation of volume-conserving isomerization mechanisms. The bicycle pedal photoisomerization is investigated using the QM/MM complete active space self-consistent field (CASSCF)/Amber force-field method. Important details about how the steric environment influences isomerization mechanisms are revealed including how the one-bond flip and hula-twist mechanisms are suppressed by the crystal cavity, the nature of the seam space in steric environments, and the features of the bicycle pedal mechanism. Specifically, in the bicycle pedal the phenyl rings of cc-DPB are locked in place and the intermolecular packing allows passageway for rotation of the central diene in a volume-conserving manner. In contrast, the bicycle pedal rotation in the gas-phase is not a stable pathway, so single-bond rotation mechanisms become operative instead. The present models, however, do not capture the quantitative activation barriers and more work is needed to better model reactions in crystals. Lastly, the reaction barriers of the different crystalline conformations within the unit cell of cc-DPB are compared to investigate the possibility for conformation-dependent isomerization. Although some difference in reaction barriers are observed, the difference is most likely not responsible for the experimentally observed periods of fast and slow conversion.

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Discovery of conical intersection mediated photochemistry with growing string methods

Cited by 34 publications

References 85 publications

The non-adiabatic nanoreactor: towards the automated discovery of photochemistry

The non-adiabatic nanoreactor: towards the automated discovery of photochemistry

Internal Conversion of the Anionic GFP Chromophore: In and Out of the I-twisted S1/S0 Conical Intersection Seam

The Mechanics of the Bicycle Pedal Photoisomerization in Crystalline cis,cis-1,4-Diphenyl-1,3-butadiene

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