On the Driving Force of the Excited-State Proton Shuttle in the Green Fluorescent Protein: A Time-Dependent Density Functional Theory (TD-DFT) Study of the Intrinsic Reaction Path

A dual experimental-theoretical perspective on ESPT photoacids and their challenges ahead

Photoacids undergo an increase in acidity upon electronic excitation, enabling excited-state proton transfer (ESPT) reactions. A multitude of compounds that allow ESPT has been identified and integrated in numerous applications, as is outlined by reviewing the rich history of photoacid research reaching back more than 90 years. In particular, achievements together with ambitions and challenges are highlighted from a combined experimental and theoretical perspective. Besides explicating the spectral signatures, transient ion-pair species, and electronic states involved in an ESPT, special emphasis is put on the diversity of methods used for studying photoacids as well as on the effects of the environment on the ESPT, illustrated in detail for 8-hydroxypyrene-1,3,6-trisulfonate (HPTS) and the naphthols as examples of prototypical photoacids. The development of exceptionally acidic super-photoacids and magic photoacids is subsequently discussed, which opens the way to applications even in aprotic solvents and provides additional insight into the mechanisms underlying ESPT. In the overview of highlights from theory, a comprehensive picture of the scope of studies on HPTS is presented, along with the general conceptualization of the electronic structure of photoacids and approaches for the quantification of excited-state acidity. We conclude with a juxtaposition of established applications of photoacids together with potential open questions and prospective research directions.

QM/MM Calculations on Excited-State Proton Transfer and Photoisomerization of a Red Fluorescent Protein mKeima with Large Stokes Shift

Large Stokes shift red fluorescent proteins (LSS-RFPs) are of growing interest for multicolor bioimaging applications. However, their photochemical mechanisms are not fully understood. Here, we employed the QM(XDW-CASPT2//CASSCF)/MM method to investigate the excited-state proton transfer and photoisomerization processes of the LSS-RFP mKeima starting from its cis neutral isomer. Upon excitation to the bright S1 state in the Franck-Condon region, mKeima relaxes to a metastable minimum-energy state. From this short-lived species, two competing deactivation pathways are available: the excited-state proton transfer in the S1 state, and the S1 decay via the S1/S0 conical intersection as a result of the cis-trans photoisomerization. In comparison, the former is a dominant excited-state relaxation pathway, leading to the cis anionic isomer of mKeima in the S1 state. This anionic intermediate then undergoes cis-trans photoisomerization after overcoming a barrier of approximately 10 kcal/mol in the S1 state, which is followed by an excited-state decay via the S1/S0 conical intersection region. The efficient nonadiabatic decay of the cis anionic isomer of mKeima in the S1 state inhibits the radiative process, leading to a weak emission around 520 nm observed experimentally. These findings shed important mechanistic light on the experimental observations and provide valuable insights that could help in the design of LSS-RFPs with superior fluorescence properties.

Non-Degenerate Two-Photon Absorption of Fluorescent Protein Chromophores

Two-photon absorption (2PA), where a pair of photons are absorbed simultaneously, is recognized as a potent bioimaging technique, which depends on the quantified 2PA probability, defined as cross-section (σ2PA). The absorbed photons either have equivalent (ω1 = ω2) or different frequencies (ω1 ≠ ω2), where the former is degenerate 2PA (D-2PA) and the latter is nondegenerate 2PA (ND-2PA). ND-2PA is of particular interest since it is a promising imaging technology with flexibility of photon frequencies and enhanced cross sections, however, it remains a relatively unexplored area compared to D-2PA. This work utilizes time-dependent density functional theory (TD-DFT) and second-order approximate coupled-cluster with the resolution-of-identity approximation (RI-CC2), for the excitation from S0 to S1, to investigate σD-2PA and σND-2PA of FP chromophore models. Interestingly, comparing CAM-B3LYP with the RI-CC2 computations shows qualitative and, in fact, near quantitative agreement in the computed improvements of σND-2PA for comparable (relative) frequency detunings, despite the known underestimations of 2PA cross sections, for TD-DFT results relative to RI-CC2 values. As expected from the 2-state model, the computed values of σND-2PA are quantitatively larger than σD-2PA, where chromophores with the largest values of σD-2PA show greater potential for σND-2PA improvement. Anionic chromophores demonstrated improvements up to 14%, while substantial enhancements were observed in neutral chromophores with some achieving a 30% increase. This work investigates the ND-2PA photophysical characteristics of FP chromophores and identifies qualitative patterns in the computed properties of ND-2PA relative to D-2PA.

Quantum dynamics of excited state proton transfer in green fluorescent protein

Photoexcitation of green fluorescent protein (GFP) triggers long-range proton transfer along a "wire" of neighboring protein residues, which, in turn, activates its characteristic green fluorescence. The GFP proton wire is one of the simplest, most well-characterized models of biological proton transfer but remains challenging to simulate due to the sensitivity of its energetics to the surrounding protein conformation and the possibility of non-classical behavior associated with the movement of lightweight protons. Using a direct dynamics variational multiconfigurational Gaussian wavepacket method to provide a fully quantum description of both electrons and nuclei, we explore the mechanism of excited state proton transfer in a high-dimensional model of the GFP chromophore cluster over the first two picoseconds following excitation. During our simulation, we observe the sequential starts of two of the three proton transfers along the wire, confirming the predictions of previous studies that the overall process starts from the end of the wire furthest from the fluorescent chromophore and proceeds in a concerted but asynchronous manner. Furthermore, by comparing the full quantum dynamics to a set of classical trajectories, we provide unambiguous evidence that tunneling plays a critical role in facilitating the leading proton transfer.

Isocyanides as Catalytic Electron Acceptors in the Visible Light Promoted Oxidative Formation of Benzyl and Acyl Radicals

The recent disclosure of the ability of aromatic isocyanides to harvest visible light and act as single electron acceptors when reacting with tertiary aromatic amines has triggered a renewed interest in their application to the development of green photoredox catalytic methodologies. Accordingly, the present work explores their ability to promote the generation of both alkyl and acyl radicals starting from radical precursors such as Hantzsch esters, potassium alkyltrifluoroborates, and α-oxoacids. Mechanistic studies involving UV-visible absorption and fluorescence experiments, electrochemical measurements of the ground-state redox potentials along with computational calculations of both the ground- and the excited-state redox potentials of a set of nine different aromatic isocyanides provide key insights to promote a rationale design of a new generation of isocyanide-based organic photoredox catalysts. Importantly, the green potential of the investigated chemistry is demonstrated by a direct and easy access to deuterium labeled compounds.

Delineating Ultrafast Structural Dynamics of a Green-Red Fluorescent Protein for Calcium Sensing

Fluorescent proteins (FPs) are indispensable tools for noninvasive bioimaging and sensing. Measuring the free cellular calcium (Ca²⁺) concentrations in vivo with genetically encodable FPs can be a relatively direct measure of neuronal activity due to the complex signaling role of these ions. REX-GECO1 is a recently developed red-green emission and excitation ratiometric FP-based biosensor that achieves a high dynamic range due to differences in the chromophore response to light excitation with and without calcium ions. Using steady-state electronic measurements (UV/Visible absorption and emission), along with time-resolved spectroscopic techniques including femtosecond transient absorption (fs-TA) and femtosecond stimulated Raman spectroscopy (FSRS), the potential energy surfaces of these unique biosensors are unveiled with vivid details. The ground-state structural characterization of the Ca²⁺-free biosensor via FSRS reveals a more spacious protein pocket that allows the chromophore to efficiently twist and reach a dark state. In contrast, the more compressed cavity within the Ca²⁺-bound biosensor results in a more heterogeneous distribution of chromophore populations that results in multi-step excited state proton transfer (ESPT) pathways on the sub-140 fs, 600 fs, and 3 ps timescales. These results enable rational design strategies to enlarge the spectral separation between the protonated/deprotonated forms and the Stokes shift leading to a larger dynamic range and potentially higher fluorescence quantum yield, which should be broadly applicable to the calcium imaging and biosensor communities.

Mapping the Complete Photocycle that Powers a Large Stokes Shift Red Fluorescent Protein

Large Stokes shift (LSS) red fluorescent proteins (RFPs) are highly desirable for bioimaging advances. The RFP mKeima, with coexisting cis- and trans-isomers, holds significance as an archetypal system for LSS emission due to excited-state proton transfer (ESPT), yet the mechanisms remain elusive. We implemented femtosecond stimulated Raman spectroscopy (FSRS) and various time-resolved electronic spectroscopies, aided by quantum calculations, to dissect the cis- and trans-mKeima photocycle from ESPT, isomerization, to ground-state proton transfer in solution. This work manifests the power of FSRS with global analysis to resolve Raman fingerprints of intermediate states. Importantly, the deprotonated trans-isomer governs LSS emission at 620 nm, while the deprotonated cis-isomer's 520 nm emission is weak due to an ultrafast cis-to-trans isomerization. Complementary spectroscopic techniques as a table-top toolset are thus essential to study photochemistry in physiological environments.

Direct or Indirect ESPT Mechanism in CFP psamFP488? A Theoretical-Computational Investigation

Fluorescent Proteins are widely studied for their multiple applications in technological and biotechnological fields. Despite this, they continue to represent a challenge in terms of a complete understanding of all the non-equilibrium photo-induced processes that rule their properties. In this context, a theoretical-computational approach can support experimental results in unveiling and understanding the processes taking place after electronic excitation. A non-standard cyan fluorescent protein, psamFP488, is characterized by an absorption maximum that is blue-shifted in comparison to other cyan fluorescent proteins. This protein is characterized by an extended Stokes shift and an ultrafast (170 fs) excited state proton transfer. In this work, a theoretical-computational study, including excited state ab initio dynamics, is performed to help understanding the reaction mechanism and propose new hypotheses on the role of the residues surrounding the chromophore. Our results suggest that the proton transfer could be indirect toward the acceptor (Glu167) and involves other residues surrounding the chromophore, despite the ultrafast kinetics.

Free Energy Profiles of Proton Transfer Reactions: Density Functional Benchmark from Biased Ab Initio Dynamics

By coupling an enhanced sampling algorithm with an orbital-localized variant of Car-Parrinello molecular dynamics, the so-called atomic centered density matrix propagation model, we reconstruct the free energy profiles along reaction pathways using different density functional approximations (DFAs) ranging from locals to hybrids. In particular, we compare the computed free energy barrier height of proton transfer (PT) reactions to those obtained by a more traditional static approach, based on the intrinsic reaction coordinate (IRC), for two case systems, namely malonaldehyde and formic acid dimer. The obtained results show that both the IRC profiles and the potentials of mean force, derived from biased dynamic trajectories, are very sensitive to the density functional approximation applied. More precisely, we observe that, with the notable exception of M06-L, local density functionals always strongly underestimate the reaction barrier heights. More generally, we find that also the shape of the free energy profile is very sensitive to the density functional choice, thus highlighting the effect, often neglected, that the choice of DFA has also in the case of dynamics simulations.

Proton Transfer from a Photoacid to a Water Wire: First Principles Simulations and Fast Fluorescence Spectroscopy

Proton transfer reactions are ubiquitous in chemistry, especially in aqueous solutions. We investigate photoinduced proton transfer between the photoacid 8-hydroxypyrene-1,3,6-trisulfonate (HPTS) and water using fast fluorescence spectroscopy and ab initio molecular dynamics simulations. Photoexcitation causes rapid proton release from the HPTS hydroxyl. Previous experiments on HPTS/water described the progress from photoexcitation to proton diffusion using kinetic equations with two time constants. The shortest time constant has been interpreted as protonated and photoexcited HPTS evolving into an "associated" state, where the proton is "shared" between the HPTS hydroxyl and an originally hydrogen bonded water. The longer time constant has been interpreted as indicating evolution to a "solvent separated" state where the shared proton undergoes long distance diffusion. In this work, we refine the previous experimental results using very pure HPTS. We then use excited state ab initio molecular dynamics to elucidate the detailed molecular mechanism of aqueous excited state proton transfer in HPTS. We find that the initial excitation results in rapid rearrangement of water, forming a strong hydrogen bonded network (a "water wire") around HPTS. HPTS then deprotonates in ≤3 ps, resulting in a proton that migrates back and forth along the wire before localizing on a single water molecule. We find a near linear relationship between the emission wavelength and proton-HPTS distance over the simulated time scale, suggesting that the emission wavelength can be used as a ruler for the proton distance. Our simulations reveal that the "associated" state corresponds to a water wire with a mobile proton and that the diffusion of the proton away from this water wire (to a generalized "solvent-separated" state) corresponds to the longest experimental time constant.

Theoretical Insights into Excited-State Intermolecular Proton Transfers of 2,7-Diazaindole in Water Using a Microsolvation Approach

The detailed excited-state intermolecular proton transfer (ESInterPT) mechanism of 2,7-diazaindole with water wires consisting of either one or two shells [2,7-DAI(H₂O)_n; n = 1-5] has been theoretically explored by time-dependent density functional theory using microsolvation with an implicit solvent model. On the basis of the excited-state potential energy surfaces along the proton transfer (PT) coordinates, among all 2,7-DAI(H₂O)_n, the multiple ESInterPT of 2,7-DAI(H₂O)₂₊₃ through the first hydration shell (inner circuit) is the most easy process to occur with the lowest PT barrier and a highly exothermic reaction. The lowest PT barrier resulted from the outer three waters pushing the inner circuit waters to be much closer to 2,7-DAI, leading to the enhanced intermolecular hydrogen-bonding strength of the inner two waters. Moreover, on-the-fly dynamic simulations show that the multiple ESInterPT mechanism of 2,7-DAI(H₂O)₂₊₃ is the triple PT in a stepwise mechanism with the highest PT probability. This solvation effect using microsolvation and dynamic simulation is a cost-effect approach to reveal the solvent-assisted multiple proton relay of chromophores based on excited-state proton transfer.

Modeling Excited-State Proton Transfer to Solvent: A Dynamics Study of a Super Photoacid with a Hybrid Implicit/Explicit Solvent Model

The rapid growth of time-resolved spectroscopies and the theoretical advances in ab initio molecular dynamics (AIMD) pave the way to look at the real-time molecular motion following the electronic excitation. Here, we exploited the capabilities of AIMD combined with a hybrid implicit/explicit model of solvation to investigate the ultrafast excited-state proton transfer (ESPT) reaction of a super photoacid, known as QCy9, in water solution. QCy9 transfers a proton to a water solvent molecule within 100 fs upon the electronic excitation in aqueous solution, and it is the strongest photoacid reported in the literature so far. Because of the ultrafast kinetics, it has been experimentally hypothesized that the ESPT escapes the solvent dynamics control (Huppert et al., J. Photochem. Photobiol. A2014,277, 90). The sampling of the solvent configuration space on the ground electronic state is the first key step toward the simulation of the ESPT event. Therefore, several configurations in the Franck–Condon region, describing an average solvation, were chosen as starting points for the excited-state dynamics. In all cases, the excited-state evolution spontaneously leads to the proton transfer event, whose rate is strongly dependent on the hydrogen bond network around the proton acceptor solvent molecule. Our study revealed that the explicit representation at least of three solvation shells around the proton acceptor molecule is necessary to stabilize the excess proton. Furthermore, the analysis of the solvent molecule motions in proximity of the reaction site suggested that even in the case of the strongest photoacid, the ESPT is actually assisted by the solvation dynamics of the first and second solvation shells of the water accepting molecule.

A Not Obvious Correlation Between the Structure of Green Fluorescent Protein Chromophore Pocket and Hydrogen Bond Dynamics: A Choreography From ab initio Molecular Dynamics

The Green Fluorescent Protein (GFP) is a widely studied chemical system both for its large amount of applications and the complexity of the excited state proton transfer responsible of the change in the protonation state of the chromophore. A detailed investigation on the structure of the chromophore environment and the influence of chromophore form (either neutral or anionic) on it is of crucial importance to understand how these factors could potentially influence the protein function. In this study, we perform a detailed computational investigation based on the analysis of ab-initio molecular dynamics simulations, to disentangle the main structural quantities determining the fine balance in the chromophore environment. We found that specific hydrogen bonds interactions directly involving the chromophore (or not), are correlated to quantities, such as the volume of the cavity in which the chromophore is embedded and that it is importantly affected by the chromophore protonation state. The cross-correlation analysis performed on some of these hydrogen bonds and the cavity volume, demonstrates a direct correlation among them and we also identified the ones specifically involved in this correlation. We also found that specific interactions among residues far in the space are correlated, demonstrating the complexity of the chromophore environment and that many structural quantities have to be taken into account to properly describe and understand the main factors tuning the active site of the protein. From an overall evaluation of the results obtained in this work, it is shown that the residues which a priori are perceived to be spectators play instead an important role in both influencing the chromophore environment (cavity volume) and its dynamics (cross-correlations among spatially distant residues).

Multiresolution continuous wavelet transform for studying coupled solute-solvent vibrations via ab initio molecular dynamics

Vibrational analysis in solution and the theoretical determination of infrared and Raman spectra are of key importance in many fields of chemical interest. Vibrational band dynamics of molecules and their sensitivity to the environment can also be captured by these spectroscopies in their time dependent version. However, it is often difficult to provide an interpretation of the experimental data at the molecular scale, such as molecular mechanisms or the processes hidden behind them. In this work, we present a theoretical-computational protocol based on ab initio molecular dynamics simulations and a combination of normal-like (generalized) mode analysis of solute-solvent clusters with a wavelet transform, for the first time. The case study is the vibrational dynamics of N-methyl-acetamide (NMA) in water solution, a well-known model of hydration of peptides and proteins. Amide modes are typical bands of peptide and protein backbone, and their couplings with the environment are very challenging in terms of the accurate prediction of solvent induced intensity and frequency shifts. The contribution of water molecules surrounding NMA to the composition of generalized and time resolved modes is introduced in our vibrational analysis, showing unequivocally its influence on the amide mode spectra. It is also shown that such mode compositions need the inclusion of the first shell solvent molecules to be accurately described. The wavelet analysis is proven to be strongly recommended to follow the time evolution of the spectra, and to capture vibrational band couplings and frequency shifts over time, preserving at the same time a well-balanced time-frequency resolution. This peculiar feature also allows one to perform a combined structural-vibrational analysis, where the different strengths of hydrogen bond interactions can quantitatively affect the amide bands over time at finite temperature. The proposed method allows for the direct connection between vibrational modes and local structural changes, providing a link from the spectroscopic observable to the structure, in this case the peptide backbone, and its hydration layouts.

Simulation of self-heating process on the nanoscale: a multiscale approach for molecular models of nanocomposite materials

A theoretical-computational protocol to model the Joule heating process in nanocomposite materials is presented. The proposed modeling strategy is based on post processing of trajectories obtained from large scale molecular simulations. This protocol, based on molecular models, is the first one to be applied to organic nanocomposites based on carbon nanotubes (CNT). This strategy allows to keep a microscopic explicit picture of the systems, to directly catch the molecular structure underlying the process under study and, at the same time, to include macroscopic boundary conditions fixed in the experiments. As validation and first application of the proposed strategy, a detailed investigation on CNT based organic composites is reported. The effect of CNT morphologies, concentration and working conditions on Joule heating has been modelled and compared with available experiments. Further experiments are performed also in this work to increase the number of comparisons especially in specific voltage ranges where available references from literature were missing. Simulations are in both qualitative and quantitative agreement with several experiments and trends reported in the recent literature, as well as with experiments performed in this work. The proposed approach combined with large scale hybrid particle-field molecular simulations can give insights and opens to way to a rational design of self-heating nanocomposites.

Ab-initio molecular dynamics and hybrid explicit-implicit solvation model for aqueous and nonaqueous solvents: GFP chromophore in water and methanol solution as case study

Solute-solvent interactions are proxies for understanding how the electronic density of a chromophore interacts with the environment in a more exhaustive way. The subtle balance between polarization, electrostatic, and non-bonded interactions need to be accurately described to obtain good agreement between simulations and experiments. First principles approaches providing accurate configurational sampling through molecular dynamics may be a suitable choice to describe solvent effects on solute chemical-physical properties and spectroscopic features, such as optical absorption of dyes. In this context, accurate energy potentials, obtained by hybrid implicit/explicit solvation methods along with employing nonperiodic boundary conditions, are required to represent bulk solvent around a large solute-solvent cluster. In this work, a novel strategy to simulate methanol solutions is proposed combining ab initio molecular dynamics, a hybrid implicit/explicit flexible solvent model, nonperiodic boundary conditions, and time dependent density functional theory. As case study, the robustness of the proposed protocol has been gauged by investigating the microsolvation and electronic absorption of the anionic green fluorescent protein chromophore in methanol and aqueous solution. Satisfactory results are obtained, reproducing the microsolvation layout of the chromophore and, as a consequence, the experimental trends shown by the optical absorption in different solvents.

An electron density based analysis to establish the electronic adiabaticity of proton coupled electron transfer reactions

Electrons and protons are the main actors in play in proton coupled electron transfer (PCET) reactions, which are fundamental in many biological (i.e., photosynthesis and enzymatic reactions) and electrochemical processes. The mechanism, energetics and kinetics of PCET reactions are strongly controlled by the coupling between the transferred electrons and protons. Concerted PCET reactions are classified according to the electronical adiabaticity degree of the process. To discriminate among different mechanisms, we propose a new analysis based on the use of electron density based indexes. We choose, as test case, the 3-Methylphenoxyl/phenol system in two different conformations to show how the proposed analysis is a suitable tool to discriminate between the different degree of adiabaticity of PCET processes. The very low computational cost of this procedure is extremely promising to analyze and provide evidences of PCET mechanisms ruling the reactivity of many biological and catalytic systems.

Mapping Structural Dynamics of Proteins with Femtosecond Stimulated Raman Spectroscopy

The structure-function relationships of biomolecules have captured the interest and imagination of the scientific community and general public since the field of structural biology emerged to enable the molecular understanding of life processes. Proteins that play numerous functional roles in cellular processes have remained in the forefront of research, inspiring new characterization techniques. In this review, we present key theoretical concepts and recent experimental strategies using femtosecond stimulated Raman spectroscopy (FSRS) to map the structural dynamics of proteins, highlighting the flexible chromophores on ultrafast timescales. In particular, wavelength-tunable FSRS exploits dynamic resonance conditions to track transient-species-dependent vibrational motions, enabling rational design to alter functions. Various ways of capturing excited-state chromophore structural snapshots in the time and/or frequency domains are discussed. Continuous development of experimental methodologies, synergistic correlation with theoretical modeling, and the expansion to other nonequilibrium, photoswitchable, and controllable protein systems will greatly advance the chemical, physical, and biological sciences.

Exploring free energy profile of petroleum thermal cracking mechanisms

Understanding the mechanisms of petroleum thermal cracking is critical to develop more efficient and eco-friendly petroleum cracking processes. Asphaltenes are the main component of petroleum subjected to cracking processes. Thermal cracking mechanisms of petroleum were explored by computational methods using 1,2-diphenylethane (DPE) as a model molecule in this study. The overall mechanisms were divided into four steps including initiation, H-transfer reaction, H-ipso reaction, and termination represented by seven reactions. We carried out extensive quantum chemistry calculations at high levels of theory to accurately explore the minimum energy pathways as the mechanisms of the proposed reactions. The reaction energy and barriers in terms of enthalpy and free energy and their temperature dependence were calculated in the vacuum and in both polar and nonpolar solvents using the polarizable continuum model (PCM) method. The temperature dependence of the target reaction barriers are characterized in different environments and provides computational guidance for future development for petroleum thermal cracking. As the first reported systematic investigation of petroleum cracking mechanisms, this study provided a comprehensive theoretical description of petroleum cracking processes with valuable information about temperature and solvent dependence. Graphical abstract.

Unveiling coupled electronic and vibrational motions of chromophores in condensed phases

The quest for capturing molecular movies of functional systems has motivated scientists and engineers for decades. A fundamental understanding of electronic and nuclear motions, two principal components of the molecular Schrödinger equation, has the potential to enable the de novo rational design for targeted functionalities of molecular machines. We discuss the development and application of a relatively new structural dynamics technique, femtosecond stimulated Raman spectroscopy with broadly tunable laser pulses from the UV to near-IR region, in tracking the coupled electronic and vibrational motions of organic chromophores in solution and protein environments. Such light-sensitive moieties hold broad interest and significance in gaining fundamental knowledge about the intramolecular and intermolecular Hamiltonian and developing effective strategies to control macroscopic properties. Inspired by recent experimental and theoretical advances, we focus on the in situ characterization and spectroscopy-guided tuning of photoacidity, excited state proton transfer pathways, emission color, and internal conversion via a conical intersection.

Role of Hydrogen Bonding in Green Fluorescent Protein-like Chromophore Emission

The fluorescence emission from green fluorescent protein (GFP) is known to be heavily influenced by hydrogen bonding between the core fluorophore and the surrounding side chains or water molecules. Yet how to utilize this feature for modulating the fluorescence of GFP chromophore or GFP-like fluorophore still remains elusive. Here we present theoretical calculations to predict how hydrogen bonding could influence the excited states of the GFP-like fluorophores. These studies provide both a new perspective for understanding the photophysical properties of GFP as well as a solid basis for the rational design of GFP-based fluorophores.

A computational study on H2S release and amide formation from thionoesters and cysteine

The recognition of the biological activity of H2S has drawn much attention to the development of biocompatible H2S release reactions. Thiol-, particularly cysteine-triggered systems which mimic the enzymatic conversion of cysteine or homocysteine to H2S have been intensively reported recently. Herein, a density functional theory (DFT) study was performed to address the reaction mechanism of H2S release and potential amide bond formation from thionoesters and cysteine to gain deeper mechanistic insights. Three possible mechanisms were considered and we found that the one starting from the nucleophilic addition of the ionized mercapto of cysteine on thionoester to generate a dithioester intermediate (Path A) is kinetically favored over the others starting from the nucleophilic addition of the amine of cysteine to generate thionoamide intermediates (Paths B and C). Dithioester then undergoes intramolecular nucleophilic addition of an amine group and the rate-limiting water-assisted proton transfer to generate a cyclic thiol intermediate, and finally affords H2S and dihydrothiazole via water-assisted elimination. The hydrolysis of thionoamide or dihydrothiazole to produce amide is highly difficult under neutral conditions but is operative under strong basic conditions, which explains the experimental observation that dihydrothiazole rather than amide is the major product. Meanwhile, the ring opening reaction of the cyclic thiol intermediate to form the more stable thionoamide is detrimental to H2S release and becomes competitive under basic conditions.

Role of Ser65, His148 and Thr203 in the Organic Solvent-dependent Spectral Shift in Green Fluorescent Protein

The photophysics of green fluorescent protein (GFP) is remarkable because of its exceptional property of excited state proton transfer (ESPT) and the presence of a functional proton wire. Another interesting property of wild-type GFP is that its absorption and fluorescence excitation spectra are sensitive to the presence of polar organic solvents even at very low concentrations. Here, we use a combination of methodologies including site-specific mutagenesis, absorption spectroscopy, steady-state and time-resolved fluorescence measurements and all-atom molecular dynamics simulations in explicit solvent, to uncover the mechanism behind the unique spectral sensitivity of GFP toward organic solvents. Based on the evidences provided herein, we suggest that organic solvent-induced changes in the proton wire prevent ground state movement of a proton through the wire and thus bring about the spectral changes observed. The present study can not only help to understand the mechanism of proton transfer by further dissecting the intricate steps in GFP photophysics but also encourages to develop GFP-based organic solvent biosensors.

Unraveling the Detailed Mechanism of Excited-State Proton Transfer

As one of the most fundamental processes, excited-state proton transfer (ESPT) plays a major role in both chemical and biological systems. In the past several decades, experimental and theoretical studies on ESPT systems have attracted considerable attention because of their tremendous potential in fluorescent probes, biological imaging, white-light-emitting materials, and organic optoelectronic materials. ESPT is related to fluorescence properties and usually occurs on an ultrafast time scale at or below 100 fs. Consequently, steady-state and femtosecond time-resolved absorption, fluorescence, and vibrational spectra have been used to explore the mechanism of ESPT. However, based on previous experimental studies, direct information, such as transition state geometries, energy barrier, and potential energy surface (PES) of the ESPT reaction, is difficult to obtain. These data are important for unravelling the detailed mechanism of ESPT reaction and can be obtained from state-of-the-art ab initio excited-state calculations. In recent years, an increasing number of experimental and theoretical studies on the detailed mechanism of ESPT systems have led to tremendous progress. This Account presents the recent advances in theoretical studies, mainly those from our group. We focus on the cases where the theoretical studies are of great importance and indispensable, such as resolving the debate on the stepwise and concerted mechanism of excited-state double proton transfer (ESDPT), revealing the sensing mechanism of ESPT chemosensors, illustrating the effect of intermolecular hydrogen bonding on the excited-state intramolecular proton transfer (ESIPT) reaction, investigating the fluorescence quenching mechanism of ESPT systems by twisting process, and determining the size of the solute·(solvent) n cluster for the solvent-assisted ESPT reaction. Through calculation of vertical excitation energies, optimization of excited-state geometries, and construction of PES of the ESPT reactions, we provide modifications to experimentally proposed mechanisms or completely new mechanism. Our proposed new and inspirational mechanisms based on theoretical studies can successfully explain the previous experimental results; some of the mechanisms have been further confirmed by experimental studies and provided guidance for researchers to design new ESPT chemosensors. Determination of the energy barrier from an accurate PES is the key to explore the ESPT mechanism with theoretical methods. This approach becomes complicated when the charge transfer state is involved for time-dependent density functional theory (TDDFT) method and optimally tuned range-separated TDDFT provides an alternative way. To unveil the driving force of ESPT reaction, the excited-state molecular dynamics combined with the intrinsic reaction coordinate calculations can be employed. These advanced approaches should be used for further studies on ESPT systems.

The mechanism of a green fluorescent protein proton shuttle unveiled in the time-resolved frequency domain by excited state ab initio dynamics

We simulated an excited state proton transfer in green fluorescent protein by excited state ab initio dynamics, and examined the reaction mechanism in both the time and the frequency domain through a multi resolution wavelet analysis. This original approach allowed us, for the first time, to directly compare the trends of photoactivated vibrations to femtosecond stimulated Raman spectroscopy results, and to give an unequivocal interpretation of the role played by low frequency modes in promoting the reaction. We could attribute the main driving force of the reaction to an important photoinduced softening of the ring-ring orientational motion of the chromophore, thus permitting the tightening of the hydrogen bond network and the opening of the reaction pathway. We also found that both the chromophore (in terms of its inter-ring dihedral angle and phenolic C-O and imidazolinone C-N bond distances) and its pocket (in terms of the inter-molecular oxygen's dihedral angle of the chromophore pocket) relaxations are modulated by low frequency (about 120 cm-1) modes involving the oxygen atoms of the network. This is in agreement with the femtosecond Raman spectroscopy findings in the time-frequency domain. Moreover, the rate in proximity to the Franck Condon region involves a picosecond time scale, with a significant influence from fluctuations of nearby hydrogen bonded residues such as His148. This approach opens a new scenario with ab initio simulations as routinely used tools to understand photoreactivity and the results of advanced time resolved spectroscopy techniques.

Nuclear quantum effect and H/D isotope effect on Cl· + (H2O)n → HCl + OH·(H2O)n−1 (n = 1–3) reactions

Cl· + (H₂O)_n → HCl + OH·(H₂O)_n−1 (n = 1–3) reactions are fundamental and important ones in atmospheric chemistry. In this study, we focused on the nuclear quantum effect (NQE) of the hydrogen nucleus on these reactions with the aid of the multicomponent quantum mechanics (MC_QM) method, which can directly take account of NQE of light nuclei. Our study reveals that the NQE of the hydrogen nucleus lowers the activation barriers of the reactions and enhances the catalytic effects of second and third water molecules. In particular, we find that (i) the NQE of the proton removes the activation barrier of the reverse reaction of HCl + OH· → Cl· + H₂O, and (ii) the catalytic effect of the third water molecule appears in only our MC_QM calculation. We also analyze the H/D isotope effects on these reactions by using the MC_QM method.

Cl·+ (H₂O)_n → HCl + OH(H₂O)_n−1 (n = 1–3) reactions have been investigated using multicomponent quantum mechanics method, which can take account of the nuclear quantum effect of proton and deuteron.