Ab initio study on electron excitation and electron transfer in tryptophan–tyrosine system

Addition of tryptophan methyl-ester on [60]fullerene: theoretical investigation of the mechanisms of azomethine ylides and fulleropyrrolidine formation

In this paper, we perform the synthesization of carbon nanoparticles for active principle vectorization, with the suggestion of a reaction mechanism of tryptophan methyl ester addition on [60]fullerene. Firstly, we studied the effect of tryptophan form on its addition reaction on [60]fullerene. So, in order to determine the preferred environment that makes this reaction the most favorable, we considered all tryptophan possible forms in our investigation: the molecular, the zwitterionic, and the dibasic forms. Secondly, we investigate the proposed reaction mechanism of tryptophan methyl ester addition on [60]fullerene using theoretical thermodynamic calculation. Our hypothesis suggests the formation of azomethine ylide molecule in a first step followed by its addition on [60]fullerene in the second step by the photo-addition reaction involving the oxygen in its singlet state. The stability of each reactive intermediate involved in this mechanism is verified thermodynamically. The 12 most stable conformations of azomethine ylide were observed through potential energy surface analysis. They were obtained by a relaxed scan of the four dihedral angles. The calculations were conducted on the optimized geometry of fulleropyrrolidine mono-adduct and the bulk values of its thermodynamic constants were also determined. Infrared spectra observed in 100-4000 cm^-1 region confirmed our hypothesis suggesting the first step of azomethine ylide formation followed by the second step of azomethine ylide addition on [60]fullerene by ν(C_aliphatic-C-N), ν(C_aromatic-C-N) and ^δ(N-H) coupled with ν(C-N) absorption bond. Graphical abstract Optimized geometry of the Fulleropyrrolidine monoaduct molecule.

Photocycle dynamics of the E149A mutant of cryptochrome 3 from Arabidopsis thaliana

The E149A mutant of the cryDASH member cryptochrome 3 (cry3) from Arabidopsis thaliana was characterized in vitro by optical absorption and emission spectroscopic studies. The mutant protein non-covalently binds the chromophore flavin adenine dinucleotide (FAD). In contrast to the wild-type protein it does not bind N5,N10-methenyl-5,6,7,8-tetrahydrofolate (MTHF). Thus, the photo-dynamics caused by FAD is accessible without the intervening coupling with MTHF. In dark adapted cry3-E149A, FAD is present in the oxidized form (FAD(ox)), semiquinone form (FADH(.)), and anionic hydroquinone form (FAD(red)H(-)). Blue-light photo-excitation of previously unexposed cry3-E149A transfers FAD(ox) to the anionic semiquinone form (FAD()(-)) with a quantum efficiency of about 2% and a back recovery time of about 10s (photocycle I). Prolonged photo-excitation leads to an irreversible protein re-conformation with structure modification of the U-shaped FAD and enabling proton transfer. Thus, a change in the photocycle dynamics occurs with photo-conversion of FAD(ox) to FADH(.), FADH(.) to FAD(red)H(-), and thermal back equilibration in the dark (photocycle II). The photocycle dynamics of cry3-E149A is compared with the photocycle behaviour of wild-type cry3 and other photo-sensory cryptochromes.

Linear and Nonlinear Optical Response of Aromatic Amino Acids: A Time-Dependent Density Functional Investigation

The linear and nonlinear optical responses of the three aromatic amino acids tryptophan, tyrosine, and phenylalanine have been investigated by time-dependent density functional theory. The effect of the peptidic chain on the polarizabilities and the first hyperpolarizabilities is addressed by substituting different groups to the chromophores indole, phenol, and benzene. The optimized structures are in very good agreement with the experimental results. Furthermore, the calculated polarizabilities are found to match well with the empirical results, showing the evolution obtained as the chain is lengthened. A systematic and constant increase of the polarizability is found, for the three chromophores, for the various chain lengths. The first hyperpolarizability is also noticeably modified by the chains, but the evolution of this quantity is found to be more dependent on the system considered. Finally, it is suggested that each of the three aromatic amino acids has a significant contribution to the nonlinear response of proteins.

Isotopic effects in the electronic spectra of tryptophan

No influence of isotopic substitution in deuterium-substituted tryptophan on the florescence excitation spectrum has previously been found out. Here, the isotopic effects of electronic excitation of deuterium-substituted tryptophan were experimentally and theoretically analyzed for first time. It was shown a short-wave shift of the UV-absorption maximum at 220 nm corresponding to the 360 cal/mol and short-wave shift for fluorescence spectrum corresponding to the 210 cal/mol. To account for this effect, the quantum chemical calculations of the geometric and electron structure, frequencies of normal vibrations and transition energies have been performed. The isotopic effects originate from the zero-point energies of ground and excited states. It was found that isotopic shifts depend on the position of isotope in the molecule and kind of transition. So, it can be utilized in the analysis of proteins structure and complexation.

Hydride Affinities of Borane Derivatives: Novel Approach in Determining the Origin of Lewis Acidity Based on Triadic Formula

The problem of intrinsic Lewis acidities of simple boron compounds (BH3-mXm, m = 0-3, X = F, Cl, Br, CH3, and OH) is assessed by their gas-phase hydride affinities (HAs). A simple and intuitively appealing picture of the interaction process including detachment of an electron from the hydride ion H-, capture of the pruned electron to the investigated Lewis acid (LA), and subsequent formation of the homolytic chemical bond between two newly created radicals is proposed. It enables transparent and straightforward dissection of the initial and final state effects, which taken together with the intermediate relaxation stabilization determine the trend of changes in the hydride affinities. The former effect is reflected in the electron affinities of the neutral Lewis acids given within Koopmans' approximation, while the final state effect involves properties of the formed Lewis acid-base adducts mirrored in the bond dissociation energy of the formed [LA-H]- chemical bond. It is demonstrated that unexpectedly low Lewis acidity of fluoroboranes relative to the corresponding chlorine and bromine derivatives can be traced down to the unfavorable Koopmans' electron affinities. Hence, it is a consequence of the initial state effect. In contrast, chloroboranes are more potent Lewis acids than fluoroboranes, because the relaxation and final state effects decisively influence their Lewis acidity. Finally, bromine-substituted borane compounds provide the most powerful studied Lewis acids. Their hydride affinities are result of a synergic interplay of the initial state, intermediate stabilization via relaxation, and final state effects. It is shown that Pearson's global hardness indices defined within his hard and soft acid-base (HSAB) principle fail to adequately predict and interpret the calculated hydride affinities.