Computational chemistry
AIMD maps GFP's excited-state proton shuttle
Open access · cc by · source: Europe PMC
TD-DFT AIMD and wavelet spectra show GFP ESPT is concerted once low-frequency chromophore modes planarize the H-bond wire.
Study at a glance
- Design
- Computational / modelling — ONIOM QM/MM AIMD of wtGFP excited-state proton transfer with wavelet spectral analysis
- N
- Five S1 trajectories; ESPT within ~1 ps in four runs — no experimental sample N
- Population
- Wild-type green fluorescent protein chromophore environment
- Outcome
- Excited-state proton-transfer timing and vibrational signatures
Structured fields used in claim comparison tables when every cited study has a complete layer.
Key findings
Four of five S1 runs transferred the proton within 1 ps (720 fs in TRJI; 350, 380, 980 fs in II–IV). O–O contacts shorten in 15–20 fs; O–H stretches redshift; C–O/C–N bands beat out of phase every ~250 fs. Twist modes drop from 146 to 101 cm–1 and His148 approaches Otyr before transfer.
Methodology
Authors ran ONIOM QM/MM Born–Oppenheimer AIMD of wtGFP in S0 and S1 (B3LYP vs TD-CAM-B3LYP) and analysed O–H, C–O/C–N and dihedral trajectories with Morlet wavelets versus FSRS.
Limitations
Kinetics are faster than the experimental 3/10 ps phases (DFT barrier underestimation, no MM polarisation); nonadiabatic hops at longer times are omitted; only four successful S1 trajectories.
How this study connects
Role on claims
Each row is a claim on a concept or method page where this paper supports, challenges, or qualifies the statement. Roles are hand-checked — not a model guess.
TD-DFT AIMD and wavelet spectra show GFP ESPT is concerted once low-frequency chromophore modes planarize the H-bond wire.
Evidence for the claim as stated.
QM/MM AIMD of wtGFP in S₁ transfers a proton in four of five runs within 1 ps (720 fs in TRJI; 350, 380 and 980 fs in II–IV). O–O contacts shorten in 15–20 fs; twist modes drop from 146 to 101 cm⁻¹. Those computed times are faster than the experimental FSRS 3/10 ps phases (DFT barrier underestimation, no MM polarisation); nonadiabatic hops at longer times are omitted.
Evidence for the claim as stated.
MD that is later tested in a cuvette is not the same deliverable as MD that stays inside the computer. Mpro peptides have micromolar IC₅₀ values; GFP AIMD proton-transfer times disagree with 3/10 ps FSRS phases; UiO-66 proton hops are invisible to time-averaged XRD. A student who says 'MD showed the mechanism' must say whether a wet observable confirmed it.
Evidence for the claim as stated.
Time-resolved Raman is the experimental counterpart AIMD tries to match for GFP’s excited-state proton shuttle. Four of five S₁ trajectories transfer the proton within 1 ps (720, 350, 380, 980 fs); O–O contacts shorten in 15–20 fs; O–H stretches redshift; C–O/C–N bands beat out of phase every ~250 fs; twist modes drop from 146 to 101 cm⁻¹. Computed kinetics are faster than the experimental 3/10 ps FSRS phases.
Evidence for the claim as stated.
Steady-state Raman of a solid and FSRS of a protein photocycle are not the same vibrational experiment. Zn-crystal Raman fingerprints ligands next to a 3.45 eV DFT gap; stibnite/carbon Raman characterises a composite whose headline is 455.8 versus 190.1 mA h g⁻¹; GFP FSRS/AIMD tracks 146 → 101 cm⁻¹ twists on a sub-picosecond shuttle. One sentence of 'Raman confirmed the material' cannot compare those papers.
Evidence for the claim as stated.
Open questions
Tensions this paper is part of
From concept pages' “where studies disagree.” Disagreement means the same question; scope means different assays, populations, or outcomes.
MD that is later tested in a cuvette is not the same deliverable as MD that stays inside the computer. Mpro peptides have micromolar IC₅₀ values; GFP AIMD proton-transfer times disagree with 3/10 ps FSRS phases; UiO-66 proton hops are invisible to time-averaged XRD. A student who says 'MD showed the mechanism' must say whether a wet observable confirmed it.
Steady-state Raman of a solid and FSRS of a protein photocycle are not the same vibrational experiment. Zn-crystal Raman fingerprints ligands next to a 3.45 eV DFT gap; stibnite/carbon Raman characterises a composite whose headline is 455.8 versus 190.1 mA h g⁻¹; GFP FSRS/AIMD tracks 146 → 101 cm⁻¹ twists on a sub-picosecond shuttle. One sentence of 'Raman confirmed the material' cannot compare those papers.
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