Fluorescent probes for investigating the internalisation and action of bioorthogonal ruthenium catalysts within Gram-positive bacteria

Bioorthogonal reactions are extremely useful for the chemical modification of biomolecules, and are already well studied in mammalian cells. In contrast, very little attention has been given to the feasibility of such reactions in bacteria. Herein we report modified coumarin dyes for monitoring the internalisation and activity of bioorthogonal catalysts in the Gram-positive bacterial species Bacillus subtilis. Two fluorophores based on 7-aminocoumarin were synthesised and characterised to establish their luminescence properties. The introduction of an allyl carbamate (R2N-COOR') group onto the nitrogen atom of two 7-aminocoumarin derivatives with different solubility led to decreased fluorescence emission intensities and remarkable blue-shifts of the emission maxima. Importantly, this allyl carbamate group could be uncaged by the bioorthogonal, organometallic ruthenium catalyst investigated in this work, to yield the fluorescent product under biologically-relevant conditions. The internalisation of this catalyst was confirmed and quantified by ICP-OES analysis. Investigation of the bacterial cytoplasm and extracellular fractions separately, following incubation of the bacteria with the two caged dyes, facilitated their localisation, as well as that of their uncaged form by catalyst addition. In fact, significant differences were observed, as only the more lipophilic dye was located inside the cells and importantly remained there, seemingly avoiding efflux mechanisms. However, the uncaged form of this dye is not retained, and was found predominantly in the extracellular space. Finally, a range of siderophore-conjugated derivatives of the catalyst were investigated for the same transformations. Even though uptake was observed, albeit less significant than for the non-conjugated version, the fact that similar intracellular reaction rates were observed regardless of the iron content of the medium supports the notion that their uptake is independent of the iron transporters utilised by Gram-positive Bacillus subtilis cells.

Structural, Electronic and NLO Properties of 6-aminoquinoline: A DFT/TD-DFT Study

A computational study based on the DFT/TD-DFT approach was performed to explore various properties of 6-aminoquinoline (6AQ). The geometrical parameters, molecular orbitals (MOs), electronic spectra, electrostatic potential, molecular surface, reactivity parameters and thermodynamic properties of 6AQ were explored. The absorption and emission spectra of 6AQ in solvents have been estimated by TD-DFT coupled with the PCM model and correlated with the available experimental results. Depending on the solvents, the computed absorption maxima of 6AQ were noticed between 327 nm - 340 nm and ascribed to [Formula: see text] transition. The simulated emission maxima were obtained between 389 to 407 nm and ascribed to [Formula: see text] transition. On increasing the solvent polarity, both the emission and absorption maxima showed a bathochromic shift. The LUMO and HOMO were localized on the entire molecule. It was observed that the lowest excited state is possibly the [Formula: see text] charge-transfer (CT) state. The natural bonding orbital (NBO) study points out that ICT plays a significant role in stabilizing the molecular system. Moreover, the NLO (nonlinear optical) properties (polarizability, first-order hyperpolarizability and dipole moment) were computed using different hybrid functionals. The estimated values indicate that 6AQ can be considered a desirable molecule for further studies of the NLO applications.

The role played by solvent polarity in regulating the competitive mechanism between ESIPT and TICT of coumarin (E-8-((4-dimethylamino-phenylimino)-methyl)-7-hydroxy-4-methyl-2H-chromen-2-one)

Excited-state intramolecular proton transfer (ESIPT) and twist intramolecular charge transfer (TICT) are the two most fundamental dynamic processes, ubiquitous in biological and chemical reactions. The excited-state properties of (E-8-((4-dimethylamino-phenylimino)-methyl)-7-hydroxy-4-methyl-2H-chromen-2-one (CDPA) in various solvents with different polarities were investigated by using steady-state and femtosecond transient absorption spectroscopy combined with DFT/TDDFT calculations. The results demonstrated that CDPA exhibited low fluorescence in polar acetonitrile (ACN) due to ESIPT but high fluorescence in nonpolar n-Hexane was attributed to intramolecular rotation blocking ESIPT. TDDFT calculations confirmed that the dramatic phenyl group torsional of CDPA in Hexane, whereas a near planar conformation in ACN solvent. The ESIPT barrier decreases regularly with the increase of solvent polarity from n-Hexane, tetrahydrofuran to ACN solvent. These results demonstrated that the ESIPT and TICT processes of CDPA are competitive mechanisms. Our work revealed the effect solvent polarity on the emission behavior and excited-state deactivation mechanism of CDPA, which could help to design and develop new polarity probe in the microenvironments.

Effect of hydrogen bond on solvation dynamics of coumarin153 in cyclohexane-phenol solvent mixtures by time-resolved optical Kerr fluorescence

Time-resolved optical Kerr fluorescence system was used to investigate time-resolved red-shift of coumarin 153 in different solvent mixtures. The mixtures included four mole fractions of phenol-cyclohexane solvents (0, 0.013, 0.08, and 0.3), and anisole-cyclohexane solvents with the mole fraction of 0.3. The measured time-resolved fluorescence showed that, in the solvent mixtures containing phenol, the time-dependent frequency shift accelerated with the increase in the mole fraction of phenol-cyclohexane mixtures. However, the time-dependent red-shift in the fluorescence was not observed in the anisole-cyclohexane mixture, the solvent polarity could not influence the spectral Stokes shift compared with phenol. The results indicated that coumarin 153 formed an excited hydrogen bond with phenol, and the excited hydrogen bond was strengthened with an increase in the mole fraction of phenol. And, these processes also suggested that the increase in the phenol ratio improves a large number of hydrogen bond formed between phenol and carbonyl group of coumarin 153, the charge distribution will be faster towards lower the free energy of the system due to the stronger dipole moment. Therefore, the corresponding solvation response in phenol-cyclohexane mixtures with higher mole fractions decays very rapidly.

Solvent effects for vertical absorption and emission processes in solution using a self-consistent state specific method based on constrained equilibrium thermodynamics

A self-consistent state specific (SS) method in the framework of TDDFT is presented to account for solvent effects on absorption and emission processes for molecules in solution. In these processes, the initial state is an equilibrium state, while the polarization of the solvent is in nonequilibrium with the electron density of the solute in the final state. Nonequilibrium solvation free energy is calculated based on a novel nonequilibrium solvation model with constrained equilibrium manipulation. The bulk solvent effects are considered using the polarizable continuum method (PCM), where the solvent-solute interaction is described with a reaction field. Molecular orbitals and orbital energies in the presence of the reaction field corresponding to the excited state are employed and the response of the solvent is not included in the TDDFT calculations. A self-consistent procedure is designed to obtain the excited state reaction field. The equations based on this new nonequilibrium solvation model in the framework of the self-consistent SS-PCM/TDDFT method for calculation of vertical absorption and emission energies are presented and implemented in the Q-Chem package. Vertical absorption and emission energies for several small molecules in solution using the newly developed code are calculated and compared with available experimental data and the results of other theoretical studies. Solvent shifts of absorption and emission energies are reasonably reproduced with this approach. The new model is a promising approach to study nonequilibrium absorption and emission processes in solution.

The application of a UHPLC system to study the formation of various chemical species by compounds undergoing efficient self-aggregation and to determine the homodimerization constants (KDM) with values in the high range of 106–1010 M−1

This work demonstrates a new concept for the use of UHPLC method for identification of the species formed by a self-aggregating compound depending on its concentration and solvent used and to determine homodimerization constants, K_DM = 10⁶–10¹⁰ M⁻¹.

Exploring excited state properties of 7-hydroxy and 7-methoxy 4-methycoumarin: a combined time-dependent density functional theory/effective fragment potential study

Hydrogen bond dynamics, C–OH bond contracting, O–H bond stretching and O–H⋯O HB strengthening reveal the ESHT in 4MU at the S₁state.

DFT/TD-DFT study of the structural and spectral properties of two forms of Rhodamine B

The absorption wavelengths of the two forms of Rhodamine B, cation and zwitterion, were investigated by Time-Dependent Density Functional Theory (TD-DFT) in combination with polarizable continuum model. The redshift in absorption spectrum of cation relative to zwitterion is attributed to strong inductive effect of carboxyphenyl group and weak electrostatic repulsion between xanthene ring and carboxyphenyl group. The absorption wavelengths of cation and zwitterion decrease linearly with increase of solvent polarity in normal alcohols since in high polar solvents electrostatic repulsion between xanthene ring and carboxyphenyl group increases and affects xanthene π conjugation system. The absorption wavelengths in water and formamide show a deviation from linear relationship because large dielectric constant hinders electrostatic repulsion between carboxyphenyl group and xanthene π system. The hydrogen bonds affect absorption wavelengths because hydrogen bonds could affect conjugation between amino N atoms and xanthene π system or electrostatic repulsion between carboxyphenyl group and xanthene ring. These results indicate electrostatic repulsion between carboxyphenyl group and xanthene ring plays a big role in determining absorption spectrum of Rhodamine B.

A TDDFT/EFP1 study on hydrogen bonding dynamics of coumarin 151 in water

Change in energy of hydrogen bonds (HBs) upon excitation, plays an important role on the spectra of chemical and biological molecules. Effective fragment potential (EFP) method of explicit water molecules embedded in polarizable continuum medium (PCM) is used for the solvation of 7-Amino-4-(trifluoromethyl)coumarin (C151). Time dependent density functional theory (TDDFT) calculations combined with EFP/PCM had been carried out to study the electronic structure and the exited state properties of C151 with five water molecules (C151-(H2O)5 complex). S0 state and S1 state geometries were optimized using DFT/TDDFT with PBE0 functional combined with cc-pVDZ basis set, the transition energies are computed with same basis set and functional. Change in HB energy is calculated using the procedure proposed by T. Nagata et al. to calculate solute-solvent interaction energy in Nagata et al. (2011). Upon photoexcitation of C151-(H2O)5 complex, A type (N⋯H-O) HB is weakened with decrease of energy by 4.37 kJ/mol, whereas B and C type (C=O⋯H-O and N-H⋯O) HBs are strengthened with increase of 5.62 and 10.21 kJ/mol energy, respectively. This study again confirmed that the intermolecular hydrogen bonds between C151 chromophore and aqueous solvents are strengthened, not cleaved upon electronic excitation.

Deactivation of 6-aminocoumarin intramolecular charge transfer excited state through hydrogen bonding

This paper presents results of the spectral (absorption and emission) and photophysical study of 6-aminocoumarin (6AC) in various aprotic hydrogen-bond forming solvents. It was established that solvent polarity as well as hydrogen-bonding ability influence solute properties. The hydrogen-bonding interactions between S₁-electronic excited solute and solvent molecules were found to facilitate the nonradiative deactivation processes. The energy-gap dependence on radiationless deactivation in aprotic solvents was found to be similar to that in protic solvents.

Study on the modulation of spectral properties of the formylperylene-methanol clusters by excited-state hydrogen bonding strengthening

In the present work, the charge transfer (CT) process within the formylperylene (FPe)-methanol (MeOH) systems facilitated by intermolecular hydrogen bonding interactions is theoretically studied in both the ground state S0 and the first singlet excited state S1. The geometric structures, electronic spectra and the infrared spectra of the FPe monomer as well as the various hydrogen-bonded FPe-MeOH complexes in both states were calculated with the density functional theory (DFT) method and time-dependent density functional theory (TD-DFT) methods, respectively. It is demonstrated that the total effect of the intermolecular hydrogen bonding between FPe and the MeOH molecules becomes strengthened in the ground state as the number of the MeOH molecules hydrogen-bonded to the FPe molecule increases from zero to three, which induces large increases in the dipole moment as well as systemic redshifts of the absorption spectra of FPe. Furthermore, upon photoexcitation of the FPe molecule, the intermolecular hydrogen bonds formed in the various hydrogen-bonded FPe-MeOH complexes are further strengthened which leads to even larger dipole moments as well as obvious redshifts of the fluorescence spectra. The calculated electronic spectra of the various hydrogen-bonded FPe-MeOH complexes are in agreement with the steady-state absorption and fluorescence spectra of FPe observed in the binary mixed solvents with different MeOH concentration. The intermolecular hydrogen bonding strengthening in both the ground and excited states are further confirmed by the infrared spectra shifts. Moreover, the vitally important role played by the intermolecular hydrogen bonding interaction and its strengthening upon electronic excitation in the CT process is discussed.

Solvatochromic properties of 3,6-di-tert-butyl-8H-indolo[3,2,1-de]acridin-8-one

The spectral and photophysical properties of newly synthesized 3,6-di-tert-butyl-8H-indolo[3,2,1-de]acridin-8-one were studied.

An intermolecular hydrogen-bonding effect on spectral and photophysical properties of 6-aminocoumarin in protic solvents

The paper presents results of the spectral (absorption and emission) and photophysical study of 6-aminocoumarin (6AC) in strong protic solvents with different hydrogen-bond acidity. The measurements of the fluorescence lifetime and quantum yield clearly show that in protic solvents intermolecular hydrogen-bonding interactions between solute and solvent molecules facilitate the nonradiative processes. It is suggested that in these solvents very efficient internal conversion due to intermolecular hydrogen-bonding is induced. A large isotope effect is found for 6AC in deuterated water.

Theoretical study on the photodegradation mechanism of nona-BDEs in methanol

Polybrominated diphenyl ethers (PBDEs) have received special environmental concern due to their potential toxicity to humans and wildlife worldwide, however, it is difficult to reveal their dominant photochemical degradation pathways by experiment. We explored the reaction mechanisms of photochemical degradation-debromination of three nona-BDEs in methanol using theoretical calculations, in which time-dependent density functional theory (TDDFT) combined with the polarizable continuum (PCM) model is applied. The selectivity of debromination was studied, and the major octa-BDE products photochemically debrominated from nona-BDEs were identified. We find that the debromination reaction results from the electronic transitions from π to σ* orbitals when nona-BDEs are exposed to UV-light in the sunlight region, at which point the two low-lying excited states for each nona-BDE are πσ*(5Br) and πσ*(4Br), which correlate to the σ* orbitals located on the penta-Br and tetra-Br substituted phenyls, respectively. Our calculations indicate that each nona-BDE may degrade to form three kinds of octa-BDE products via the πσ*(5Br) state, whereas only one kind of octa-BDEs can be formed via the πσ*(4Br) state. Our calculations can interpret the recent experiments successfully.