Anastasia V. Bochenkova

Gas Phase Absorption Studies of Photoactive Yellow Protein Chromophore Derivatives

Photoabsorption spectra of deprotonated trans p-coumaric acid and two of its methyl substituted derivatives have been studied in gas phase both experimentally and theoretically. We have focused on the spectroscopic effect of the location of the two possible deprotonation sites on the trans p-coumaric acid which originate to either a phenoxide or a carboxylate. Surprisingly, the three chromophores were found to have the same absorption maximum at 430 nm, in spite of having different deprotonation positions. However, the absorption of the chromophore in polar solution is substantially different for the distinct deprotonation locations. We also report on the time scales and pathways of relaxation after photoexcitation for the three photoactive yellow protein chromophore derivatives. As a result of these experiments, we could detect the phenoxide isomer within the deprotonated trans p-coumaric acid in gas phase; however, the occurrence of the carboxylate is uncertain. Several computational methods were used simultaneously to provide insights and assistance in the interpretation of our experimental results. The calculated excitation energies S(0)-S(1) are in good agreement with experiment for those systems having a negative charge on a phenoxide moiety. Although our augmented multiconfigurational quasidegenerate perturbation theory calculations agree with experiment in the description of the absorption spectrum of anions with a carboxylate functional group, there are some puzzling disagreements between experiment and some calculational methods in the description of these systems.

Characterization of a complete cycle of acetylcholinesterase catalysis by ab initio QM/MM modeling

AbstractThe reaction mechanism of acetylcholine hydrolysis by acetylcholinesterase, including both acylation and deacylation stages from the enzyme-substrate (ES) to the enzyme-product (EP) molecular complexes, is examined by using an ab initio type quantum mechanical – molecular mechanical (QM/MM) approach. The density functional theory PBE0/aug-6–31+G* method for a fairly large quantum part trapped inside the native protein environment, and the AMBER force field parameters in the molecular mechanical part are employed in computations. All reaction steps, including the formation of the first tetrahedral intermediate (TI1), the acylenzyme (EA) complex, the second tetrahedral intermediate (TI2), and the EP complex, are modeled at the same theoretical level. In agreement with the experimental rate constants, the estimated activation energy barrier of the deacylation stage is slightly higher than that for the acylation phase. The critical role of the non-triad Glu202 amino acid residue in orienting lytic water molecule and in stabilizing the second tetrahedral intermediate at the deacylation stage of the enzymatic process is demonstrated. FigureThe computed energy diagram for the reaction path from the enzyme – substrate complex (ES) to the enzyme-product complex (EP).

Ultrafast dual photoresponse of isolated biological chromophores: link to the photoinduced mode-specific non-adiabatic dynamics in proteins

The anionic wild-type Green Fluorescent Protein (GFP) chromophore defines an entire class of naturally occurring chromophores, which are based on the oxydized tyrosine side chain. The GFP chromophore exhibits an enriched photoinduced non-adiabatic dynamics in the multiple excited-state decay channels. Deactivation includes vibrational resonant photodetachment and internal conversion. Here, we provide detailed insight into the efficiency of different vibrational modes in promoting a selective photoresponse in the bare GFP chromophore anion. We introduce a general theoretical model that is capable of accounting for the alternative non-equivalent pathways in internal conversion, and we outline the factors, by which the photo-initiated response may be altered in this channel. The topography around the planar minimum in S1 and the two distinct types of the S1/S0 conical intersections obtained through high-level ab initio calculations provide direct support to the proposed model. There are mode-selective ways to control the photoresponse and to direct it towards a single excited-state decay channel. By tuning the excitation wavelength, the photoresponse may be directed towards the ultrafast non-statistical electron emission coupled with vibrational (de)coherence, whereas a vibrational pre-excitation in the ground state may lead to the ultrafast non-statistical internal conversion through a conical intersection. We also discuss the implication of our results to the photo-initiated non-adiabatic dynamics in the proteins.

Hybrid diatomics-in-molecules-based quantum mechanical/molecular mechanical approach applied to the modeling of structures and spectra of mixed molecular clusters Arn(HCl)m and Arn(HF)m

A new hybrid QM/DIM approach aimed at describing equilibrium structures and spectroscopic properties of medium size mixed molecular clusters is developed. This methodology is applied to vibrational spectra of hydrogen chloride and hydrogen fluoride clusters with up to four monomer molecules embedded in argon shells Arn(H(Cl/F))m (n = 1-62, m = 1-4). The hydrogen halide complexes (QM part) are treated at the MP2/aug-cc-pVTZ level, while the interaction between HX molecules and Ar atoms (MM part) is described in terms of the semiempirical DIM methodology, based on the proper mixing between neutral and ionic states of the system [Grigorenko et al., J. Chem. Phys. 104, 5510 (1996)]. A detailed analysis of the resulting topology of the QM/DIM potential energy (hyper-)surface in the triatomic subsystem Ar-HX reveals more pronounced nonadditive atomic induction and dispersion contributions to the total interaction energy in the case of the Ar-HCl system. An extension of the original analytical DIM-based potential in the frame of the present model as well as the current limitations of the method are discussed. A modified algorithm for the gradient geometry optimization, along with partly analytical force constant matrix evaluation, is developed to treat large cages of argon atoms around molecular clusters. Calculated frequency redshifts of HX stretching vibrations in the mixed clusters relative to the isolated hydrogen-bonded complexes are in good agreement with experimental findings.

Modeling photoabsorption of the asFP595 chromophore.

The fluorescent protein asFP595 is a promising photoswitchable biomarker for studying processes in living cells. We present the results of a high level theoretical study of photoabsorption properties of the model asFP595 chromophore molecule in biologically relevant protonation states: anionic, zwitterionic, and neutral. Ground state equilibrium geometry parameters are optimized in the PBE0/(aug)-cc-pVDZ density functional theory approximation. An augmented version of multiconfigurational quasidegenerate perturbation theory (aug-MCQDPT2) following the state-averaged CASSCF/(aug)-cc-pVDZ calculations is used to estimate the vertical S0-S1 excitation energies for all chromophore species. An accuracy of this approach is validated by comparing the computed estimates of the S0-S1 absorption maximum of the closely related chromophore from the DsRed protein to the known experimental value in the gas phase. An influence of the CASSCF active space on the aug-MCQDPT2 excitation energies is analyzed. The zwitterionic form of the asFP595 chromophore is found to be the most sensitive to a particular choice and amount of active orbitals. This observation is explained by the charge-transfer type of the S0-S1 transition involving the entire conjugated pi-electron system for the zwitterionic protonation state. According to the calculation results, the anionic form in the trans conformation is found to possess the most red-shifted absorption band with the maximum located at 543 nm. The bands of the zwitterionic and neutral forms are considerably blue-shifted compared to those of the anionic form. These conclusions are at variance with the results obtained in the TDDFT approximation for the asFP595 chromophore. The absorption wavelengths computed in the aug-MCQDPT2/CASSCF theory are as follows: 543 (535), 470 (476), and 415 (417) nm for the anionic, zwitterionic, and neutral forms of the trans and cis (in parentheses) isomers of the asFP595 chromophore. These data can be used as a reference for further theoretical studies of the asFP595 chromophore in different media and for modeling photoabsorption properties of the asFP595 fluorescent protein.

UV excited-state photoresponse of biochromophore negative ions.

Members of the green fluorescent protein (GFP) family may undergo irreversible phototransformation upon irradiation with UV light. This provides clear evidence for the importance of the higher-energy photophysics of the chromophore, which remains essentially unexplored. By using time-resolved action and photoelectron spectroscopy together with high-level electronic structure theory, we directly probe and identify higher electronically excited singlet states of the isolated para- and meta-chromophore anions of GFP. These molecular resonances are found to serve as a doorway for very efficient electron detachment in the gas phase. Inside the protein, this band is found to be resonant with the quasicontinuum of a solvated electron, thus enhancing electron transfer from the GFP to the solvent. This suggests a photophysical pathway for photoconversion of the protein, where GFP resonant photooxidation in solution triggers radical redox reactions inside these proteins.

Modeling of the structure and electronic spectra of green fluorescent protein chromophore

The structure and electronic absorption spectra of a model green fluorescent protein chromophore were studied in the neutral, cationic, and anionic forms in the isolated state. The energies of S0-S1 vertical transitions were calculated using a new method based on a modified multiconfiguration quasi-degenerate perturbation theory (aug-MCQDPT2). This method was used to obtain quantitative estimates of S0-S1 vertical transition energies for chromophores in the isolated state, 2.54, 3.12, and 3.11 eV (the experimental values were 2.59, 3.05, and 2.99 eV) for the anionic, cationic, and neutral forms, respectively.

Modeling reaction routes from rhodopsin to bathorhodopsin

The quantum mechanical–molecular mechanical (QM/MM) theory was applied to calculate accurate structural parameters, vibrational and optical spectra of bathorhodopsin (BATHO), one of the primary photoproducts of the functional cycle of the visual pigment rhodopsin (RHO), and to characterize reaction routes from RHO to BATHO. The recently resolved crystal structure of BATHO (PDBID: 2G87) served as an initial source of coordinates of heavy atoms. Protein structures in the ground electronic state and vibrational frequencies were determined by using the density functional theory in the PBE0/cc‐pVDZ approximation for the QM part and the AMBER force field parameters in the MM part. Calculated and assigned vibrational spectra of both model protein systems, BATHO and RHO, cover three main regions referring to the hydrogen‐out‐of‐plan (HOOP) motion, the CC ethylenic stretches, and the CC single‐bond stretches. The S0–S1 electronic excitation energies of the QM part, including the chromophore group in the field of the protein matrix, were estimated by using the advanced quantum chemistry methods. The computed structural parameters as well as the spectral bands match perfectly the experimental findings. A structure of the transition state on the S0 potential energy surface for the ground electronic state rearrangement from RHO to BATHO was located proving a possible route of the thermal protein activation to the primary photoproduct. Proteins 2010.

HArF in Solid Argon Revisited: Transition from Unstable to Stable Configuration

The thermal conversion of HArF configurations in solid argon has been investigated both experimentally and theoretically. The matrix isolation experiments have been concentrated on temperatures 25-27 K, promoting the transition from the unstable to stable HArF configuration. The combined quantum mechanical-molecular mechanical and temperature-accelerated dynamics approach has been developed to study the real-time evolution of HArF trapped in different matrix-site morphologies. Two realistic pathways of the stable HArF formation are found for annealing at 25-27 K. The conversion mechanism in both pathways involves the local mobility of matrix vacancies in the vicinity of the HArF molecule. These two relaxation processes occurring within different timescales can cause the multiexponential decay of unstable HArF observed experimentally. The theoretical values of the activation energy of 64 meV as well as the corresponding pre-exponential factor of exp(28) s(-1), obtained for one of the unstable HArF configurations, are well consistent with the experimental estimates of 70 meV and exp(30 +/- 3) s(-1), respectively.

Photodissociation pathways and lifetimes of protonated peptides and their dimers

Photodissociation lifetimes and fragment channels of gas-phase, protonated YA(n) (n = 1,2) peptides and their dimers were measured with 266 nm photons. The protonated monomers were found to have a fast dissociation channel with an exponential lifetime of ~200 ns while the protonated dimers show an additional slow dissociation component with a lifetime of ~2 μs. Laser power dependence measurements enabled us to ascribe the fast channel in the monomer and the slow channel in the dimer to a one-photon process, whereas the fast dimer channel is from a two-photon process. The slow (1 photon) dissociation channel in the dimer was found to result in cleavage of the H-bonds after energy transfer through these H-bonds. In general, the dissociation of these protonated peptides is non-prompt and the decay time was found to increase with the size of the peptides. Quantum RRKM calculations of the microcanonical rate constants also confirmed a statistical nature of the photodissociation processes in the dipeptide monomers and dimers. The classical RRKM expression gives a rate constant as an analytical function of the number of active vibrational modes in the system, estimated separately on the basis of the equipartition theorem. It demonstrates encouraging results in predicting fragmentation lifetimes of protonated peptides. Finally, we present the first experimental evidence for a photo-induced conversion of tyrosine-containing peptides into monocyclic aromatic hydrocarbon along with a formamide molecule both found in space.