Amine-Reactive BODIPY Dye: Spectral Properties and Application for Protein Labeling

A boron-dipyrromethene (BODIPY) derivative reactive towards amino groups of proteins (NHS-Ph-BODIPY) was synthesized. Spectroscopic and photophysical properties of amine-reactive NHS-Ph-BODIPY and its non-reactive precursor (COOH-Ph-BODIPY) in a number of organic solvents were investigated. Both fluorescent dyes were characterized by green absorption (521–532 nm) and fluorescence (538–552 nm) and medium molar absorption coefficients (46,500–118,500 M⁻¹·cm⁻¹) and fluorescence quantum yields (0.32 – 0.73). Solvent polarizability and dipolarity were found to play a crucial role in solvent effects on COOH-Ph-BODIPY and NHS-Ph-BODIPY absorption and emission bands maxima. Quantum-chemical calculations were used to show why solvent polarizability and dipolarity are important as well as to understand how the nature of the substituent affects spectroscopic properties of the fluorescent dyes. NHS-Ph-BODIPY was used for fluorescent labeling of a number of proteins. Conjugation of NHS-Ph-BODIPY with bovine serum albumin (BSA) resulted in bathochromic shifts of absorption and emission bands and noticeable fluorescence quenching (about 1.5 times). It was demonstrated that the sensitivity of BSA detection with NHS-Ph-BODIPY was up to eight times higher than with Coomassie brilliant blue while the sensitivity of PII-like protein PotN (PotN) detection with NHS-Ph-BODIPY and Coomassie brilliant blue was almost the same. On the basis of the molecular docking results, the most probable binding sites of NHS-Ph-BODIPY in BSA and PotN and the corresponding binding free energies were estimated.     

Electronic structure of saturated hydrocarbons in the semi-empirical equivalent orbital method

The problem of obtaining the matrix elements of Hartree-Fock Hamiltonians for alkanes using the EO method is considered. It has been shown that the data on the electronic structure of diamond together witht ₁/e splitting in the neopentane photoelectron spectrum are helpful to produce such EO method parameter scale which involves even “through space” interactions. In terms of the EO method the photoelectron spectra of propane, butane, isobutane, and neopentane are interpreted. The valence band structure of polyethylene in analytical form is obtained.     

Synthesis of unique cagelike thiacalix[4]arene derivatives in a 1,3-alternate conformation

A novel type of doubly bridged thiacalix[4]arenes in the 1,3-alternate conformation has been prepared by direct aminolysis reaction of easily accessible thiacalix[4]arene tetraacetates with alpha,omega-diamines. Despite the high excess of diamine, both sites of a 1,3-alternate conformer can be intramolecularly bridged to form the cagelike structures in high yields. Optimum results were obtained using 1,2-ethanediamine as bridging units. X-ray analysis of the novel cagelike molecules revealed a highly preorganized array of -C(O)-NH- bonds pointing to the interior of the cavity.     

New single source route to the molybdenum nitride Mo(2)N

Dispersed Mo(2)N with lamellar morphology and high specific surface area was obtained from the decomposition of the (HMT)(2)(NH(4))(4)Mo(7)O(24) salt (HMT = hexamethylentertramine) in the temperature range 550-800 degrees C. During the thermal decomposition, reduction of Mo species by carbon from the HMT ligand occurs, with release of CO gas.     

Separation of enantiomers in capillary electrophoresis with contactless conductivity detection

Contactless conductivity detection is successfully demonstrated for the enantiomeric separation of basic drugs and amino acids in capillary electrophoresis (CE). Derivatization of the compounds or the addition of a visualization agent as for indirect optical detection schemes were not needed. Non-charged chiral selectors were employed, hydroxypropylated cyclodextrin (CD) for the more lipophilic basic drugs and 18-crown-6-tetracarboxylic acid (18C6H4) for the amino acids. Acidic buffer solutions based on lactic or citric acid were used. The detection limits were determined as 0.3 microM for pseudoephedrine as an example of a basic drug and were in the range from 2.5 to 20 microM for the amino acids.     

Molecular Structure,Thermodynamic and Spectral Characteristics of Metal-Free and Nickel Complex of Tetrakis(1,2,5-thiadiazolo)porphyrazine

The Knudsen effusion method with mass spectrometric control of the vapor composition was used to study the possibility of a congruent transition to the gas phase and to estimate the enthalpy of sublimation of metal-free tetrakis(1,2,5-thiadiazolo)porphyrazine and its nickel complex (H₂TTDPz and NiTTDPz, respectively). The geometrical and electronic structure of H₂TTDPz and NiTTDPz in ground and low-lying excited electronic states were determined by DFT calculations. The electronic structure of NiTTDPz was studied by the complete active space (CASSCF) method, following accounting dynamic correlation by multiconfigurational quasi-degenerate second-order perturbation theory (MCQDPT2). A geometrical structure of D_2h and D_4h symmetry was obtained for H₂TTDPz and NiTTDPz, respectively. According to data obtained by the MCQDPT2 method, the nickel complex possesses the ground state ¹A_1g, and the wave function of the ground state has the form of a single determinant. Electronic absorption and vibrational (IR and resonance Raman) spectra of H₂TTDPz and NiTTDPz were studied experimentally and simulated theoretically.     

Harnessing a ratiometric fluorescence output from a sensor array

Ratiometric fluorescence-based sensors are widely sought after because they can effectively convert even relatively small changes in optical output into a strong and easy-to-read signal. However, ratiometric sensor molecules are usually difficult to make. We present a proof-of-principle experiment that shows that efficient ratiometric sensing may be achieved by an array of two chromophores, one providing an on-to-off response and the second yielding an off-to-on response in a complementary fashion. In the case that both chromophores emit light of different color, the result is a switching of colors that may be utilized in the same way as from a true ratiometric probe. The chromophore array comprises two sensor elements: i) a polyurethane membrane with embedded N-anthracen-9-yl-methyl-N-7-nitrobenzoxa-[1,2,5]diazo-4-yl-N',N'-dimethylethylenediamine hydrochloride and ii) a membrane with N,N-dimethyl-N'-(9-methylanthracenyl)ethylenediamine. A combination of photoinduced electron transfer (PET) and fluorescence resonance energy transfer (FRET) allows for green-to-blue emission switching in the presence of Zn(II) ions. The sensing experiments carried out with different Zn(II) salts at controlled pH revealed that the degree of color switching in the individual sensor elements depends on both the presence of Zn(II) ions and the counter anion. These results suggest that sensing of both cations and anions may perhaps be extended to different cation-anion pairs.     

Structure of isolated tryptophyl-glycine dipeptide and tryptophyl-glycyl-glycine tripeptide: ab initio SCC-DFTB-D molecular dynamics simulations and high-level correlated ab initio quantum chemical calculations

The tryptophyl-glycine (Trp-Gly) and tryptophyl-glycyl-glycine (Trp-Gly-Gly) peptides have been studied by means of molecular dynamic simulations combined with high-level correlated ab initio quantum chemical and statistical thermodynamic calculations. The lowest energy conformers were localized in the free energy surface. The structures of the different Trp-Gly and Trp-Gly-Gly conformers coexisting in the gas phase have been for the first time reported and their scaled theoretical IR spectra unambiguously assigned and compared with previous gas-phase experimental results. Common geometrical features have been systematically observed for the sequence Trp, Trp-Gly, and Trp-Gly-Gly. In addition, the peptide backbone of Trp-Gly-Gly has been compared with that of the previously studied Phe-Gly-Gly (Reha, D. et. al. Chem. Eur. J. 2005, 11, 6803). From the observed systematic structural behavior between these peptide analogues, it is expected that the gas-phase conformers of other similar aromatic small peptides would present equivalent geometries. The DFT methodology failed to describe the potential energy surface of the studied peptides since the London dispersion energy (not covered in DFT) plays a significant role in the stabilization of most stable conformers.     

A numerical method to boundary value problems for second order delay differential equations

Summary In the first part of this paper we are dealing with theoretical statements and conditions which lead to existence and uniqueness of the solution of a nonlinear boundary value problem with delay. Next we apply this method successfully to a numerical example. The computations have been carried out at the computer Siemens 4004. The data obtained are presented in two tables.     

Vibrational spectroscopic studies and ab initio calculations of 2-cyanophenylisocyanid dichloride

FT-Raman and FT-IR spectra of 2-cyanophenylisocyanid dichloride were recorded and analyzed. The vibrational frequencies of the title compound have been computed using the Hartree-Fock/6-31G* basis and compared with the experimental values. The prepared compound was identified by NMR and mass spectra.