Elucidating the Photoprotection Mechanism of Eumelanin Monomers

Eumelanin, the functional polymer in human skin, forms a heterogeneous layered structure intrinsic to its broadband monotonic spectra. The inherent structural heterogeneity of eumelanin makes the photoprocesses very complex and diverse in nature. Due to this diversity, a complete mechanistic picture of these photoprocesses, essential to understanding the photoprotective properties, has been missing to date. In this study, we recreate the potential energy surfaces of the low-lying excited states of the multiple monomeric forms of eumelanin constituents that play a prominent role in either photoprotection or photodamage pathways. Our results indicate a diverse set of pathways for the photoexcited species to relax back to the ground state, that depends on the specific monomeric form. Furthermore, the excited state reaction channels show the scope of extensive interconversion between the different monomers and therefore, we propose that the heterogeneity of eumelanin is key to its photoprotection capability

Ionization-Induced Tautomerization in Cytosine and Effect of Solvation

The recent observation of excitation-induced tautomerization in gas-phase cytosine motivated us to investigate the possibility of facile tautomerization in ionized cytosine and the effect of solvation on the tautomerization barriers. The tautomerization mechanisms were characterized at the density functional theory (DFT)/ωB97X-D and coupled-cluster singles and doubles (CCSD) levels of theory. Vertical and adiabatic ionization energies (VIEs and AIEs, respectively) of the tautomers of cytosine and the microsolvated species were calculated with the equation-of-motion ionization-potential coupled-cluster (EOM-IP-CCSD) method. We observed that, in microsolvated cytosine, the solvatochromic shifts of the VIEs can be both blue- and red-shifted depending on the tautomers. This is explained by the analysis of the charge–dipole interactions between the cytosine and water molecules. We noticed that, upon ionization, gas-phase tautomerization barriers are reduced by 0–4 kcal/mol, whereas microsolvated (with one water) tautomerization barriers are reduced by 4–5 kcal/mol. We also investigated the tautomerization process in solvation using a continuum model with one active water molecule in the quantum mechanical region. We noticed that, even though bulk solvation has a significant effect on ionization energies, its effect on the ionization-induced tautomerization barrier is minimal

Effect of Solvation on Electron Detachment and Excitation Energies of a Green Fluorescent Protein Chromophore Variant

Hybrid quantum mechanics/molecular mechanics (QM/MM) is applied to the fluorinated green fluorescent protein (GFP) chromophore (DFHBDI) in its deprotonated form to understand the solvatochromic shifts in its vertical detachment energy (VDE) and vertical excitation energy (VEE). This variant of the GFP chromophore becomes fluorescent in an RNA environment and has a wide range of applications in biomedical and biochemical fields. From microsolvation studies, we benchmark (with respect to full QM) the accuracy of our QM/MM calculations with effective fragment potential (EFP) as the MM method of choice. We show that while the solvatochromic shift in the VEE is minimal (0.1 eV blue shift) and its polarization component is only 0.03 eV, the effect of the solvent on the VDE is quite large (3.85 eV). We also show by accurate calculations on the solvatochromic shift of the VDE that polarization accounts for ∼0.23 eV and therefore cannot be neglected. The effect of the counterions on the VDE of the deprotonated chromophore in solvation is studied in detail, and a charge-smearing scheme is suggested for charged chromophores

Electrostatic Origin of the Red Solvatochromic Shift of DFHBDI in RNA Spinach

Interactions with the environment tune the spectral properties of biological chromophores, e.g., fluorescent proteins. Understanding the relative contribution of the various types of noncovalent interactions in the spectral shifts can provide rational design principles toward developing new fluorescent probes. In this work, we investigate the origin of the red shift in the absorption spectra of the difluoro hydroxy­benzyl­idene dimethyl imida­zoli­none (DFHBDI) chromophore in RNA spinach as compared to the aqueous solution. We systematically decompose the effects of various components of interactions, namely, stacking, hydrogen bonding, and long-range electrostatics, in order to elucidate the relative role of these interactions in the observed spectral behavior. We find that the absorption peak of DFHBDI is red-shifted by ∼0.35 eV in RNA relative to the aqueous solution. Earlier proposals from Huang and co-workers have implicated the stacking interactions between DFHBDI and nucleic acid bases to be the driving force behind the observed red shift. In contrast, our findings reveal that the long-range electrostatic interactions between DFHBDI and negatively charged RNA make the most significant contribution. Moreover, we notice that the opposing electrostatic fields due to the RNA backbone and the polarized water molecules around the RNA give rise to the resultant red shift. Our results emphasize the effect of strong heterogeneity in the various environmental factors that might be competing with each other

Feasibility of Ionization-Mediated Pathway for Ultraviolet-Induced Melanin Damage

Melanin is the pigment found in human skin that is responsible for both photoprotection and photodamage. Recently there have been reports that greater photodamage of DNA occurs when cells containing melanin are irradiated with ultraviolet (UV) radiation, thus suggesting that the photoproducts of melanin cause DNA damage. Photoionization processes have also been implicated in the photodegradation of melanin. However, not much is known about the oxidation potential of melanin and its monomers. In this work we calculate the ionization energies of monomers, dimers, and few oligomers of eumelanin to estimate the threshold energy required for the ionization of eumelanin. We find that this threshold is within the UV-B region for eumelanin. We also look at the charge and spin distributions of the various ionized states of the monomers that are formed to understand which of the ionization channels might favor monomerization from a covalent dimer

Toward Understanding the Redox Properties of Model Chromophores from the Green Fluorescent Protein Family: An Interplay between Conjugation, Resonance Stabilization, and Solvent Effects

The redox properties of model chromophores from the green fluorescent protein family are characterized computationally using density functional theory with a long-range corrected functional, the equation-of-motion coupled-cluster method, and implicit solvation models. The analysis of electron-donating abilities of the chromophores reveals an intricate interplay between the size of the chromophore, conjugation, resonance stabilization, presence of heteroatoms, and solvent effects. Our best estimates of the gas-phase vertical/adiabatic detachment energies of the deprotonated (i.e., anionic) model red, green, and blue chromophores are 3.27/3.15, 2.79/2.67, and 2.75/2.35 eV, respectively. Vertical/adiabatic ionization energies of the respective protonated (i.e., neutral) species are 7.64/7.35, 7.38/7.15, and 7.70/7.32 eV, respectively. The standard reduction potentials (<i>E</i>_red⁰) of the anionic (Chr^•/Chr^–) and neutral (Chr^+•/Chr) model chromophores in acetonitrile are 0.34/1.40 V (red), 0.22/1.24 V (green), and −0.12/1.02 V (blue), suggesting, counterintuitively, that the red chromophore is more difficult to oxidize than the green and blue ones (in both neutral and deprotonated forms). The respective redox potentials in water follow a similar trend but are more positive than the acetonitrile values

A VUV Photoionization and Ab Initio Determination of the Ionization Energy of a Gas-Phase Sugar (Deoxyribose)

The ionization energy of gas-phase deoxyribose was determined using tunable vacuum ultraviolet synchrotron radiation coupled to an effusive thermal source. Adiabatic and vertical ionization energies of the ground and first four excited states of α-pyranose, the structure that dominates in the gas phase, were calculated using high-level electronic structure methods. An appearance energy of 9.1(±0.05) eV was recorded, which agrees reasonably well with a theoretical value of 8.8 eV for the adiabatic ionization energy. A clear picture of the dissociative photoionization dynamics of deoxyribose emerges from the fragmentation pattern recorded using mass spectrometry and from ab initio molecular dynamics calculations. The experimental threshold 9.4 (±0.05) eV for neutral water elimination upon ionization is captured well in the calculations, and qualitative insights are provided by molecular orbital analysis and molecular dynamics snapshots along the reaction coordinate

What Drives the Redox Properties of Model Green Fluorescence Protein Chromophores?

We report the first experimental determination of the oxidation potentials <i>E</i>_ox⁰ (relative to the standard hydrogen electrode, SHE) of model green fluorescent protein (GFP) chromophores. Para-, meta, and ortho-hydroxy (4-hydroxybenzylidene-2,3-dimethylimidazolinone, HBDI) and methoxy (MeOBDI) derivatives were studied. <i>E</i>_ox⁰ of the three isomers in acetonitrile are −1.31, −1.52, and −1.39 V, respectively. Electronic structure calculations reproduce the observed differences between the isomers and reveal that <i>E</i>_ox⁰ follows the ionization energies (IEs), that is, p-MeOBDI has the lowest IE (6.96 eV in the gas phase) due to resonance stabilization of its cation, whereas the resonance is detuned in m-MeOBDI, resulting in more-negative <i>E</i>_ox⁰. The observed meta and ortho effects in <i>E</i>_ox⁰ are similar to the trends in p<i>K</i>_a. The effect of increased solvent polarity on absolute <i>E</i>_ox⁰ (and especially on para-meta-ortho differences) was found to be small. The redox properties of GFP chromophores are driven by their structure and can be correlated with IEs, which can be exploited in predicting the properties of other fluorescent protein chromophores

First-Principle Protocol for Calculating Ionization Energies and Redox Potentials of Solvated Molecules and Ions: Theory and Application to Aqueous Phenol and Phenolate

The effect of hydration on the lowest vertical ionization energy (VIE) of phenol and phenolate solvated in bulk water was characterized using the equation-of-motion ionization potential coupled-cluster (EOM-IP-CCSD) and effective fragment potential (EFP) methods (referred to as EOM/EFP) and determined experimentally by valence photoemission measurements using microjets and synchrotron radiation. The computed solvent-induced shifts in VIEs (ΔVIEs) are −0.66 and +5.72 eV for phenol and phenolate, respectively. Our best estimates of the absolute values of VIEs (7.9 and 7.7 eV for phenol and phenolate) agree reasonably well with the respective experimental values (7.8 ± 0.1 and 7.1 ± 0.1 eV). The EOM/EFP scheme was benchmarked against full EOM-IP-CCSD using microsolvated phenol and phenolate clusters. A protocol for calculating redox potentials with EOM/EFP was developed based on linear response approximation (LRA) of free energy determination. The oxidation potentials of phenol and phenolate calculated using LRA and EOM/EFP are 1.32 and 0.89 V, respectively; they agree well with experimental values

Extension of the Effective Fragment Potential Method to Macromolecules

The effective fragment potential (EFP) approach, which can be described as a nonempirical polarizable force field, affords an accurate first-principles treatment of noncovalent interactions in extended systems. EFP can also describe the effect of the environment on the electronic properties (e.g., electronic excitation energies and ionization and electron-attachment energies) of a subsystem via the QM/EFP (quantum mechanics/EFP) polarizable embedding scheme. The original formulation of the method assumes that the system can be separated, without breaking covalent bonds, into closed-shell fragments, such as solvent and solute molecules. Here, we present an extension of the EFP method to macromolecules (mEFP). Several schemes for breaking a large molecule into small fragments described by EFP are presented and benchmarked. We focus on the electronic properties of molecules embedded into a protein environment and consider ionization, electron-attachment, and excitation energies (single-point calculations only). The model systems include chromophores of green and red fluorescent proteins surrounded by several nearby amino acid residues and phenolate bound to the T4 lysozyme. All mEFP schemes show robust performance and accurately reproduce the reference full QM calculations. For further applications of mEFP, we recommend either the scheme in which the peptide is cut along the C_α–C bond, giving rise to one fragment per amino acid, or the scheme with two cuts per amino acid, along the C_α–C and C_α–N bonds. While using these fragmentation schemes, the errors in solvatochromic shifts in electronic energy differences (excitation, ionization, electron detachment, or electron-attachment) do not exceed 0.1 eV. The largest error of QM/mEFP against QM/EFP (no fragmentation of the EFP part) is 0.06 eV (in most cases, the errors are 0.01–0.02 eV). The errors in the QM/molecular mechanics calculations with standard point charges can be as large as 0.3 eV