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61.
Ksenia V. Ksenofontova Anastasia A. Kerner Alexander A. Ksenofontov Artyom Yu. Shagurin Pavel S. Bocharov Michael M. Lukanov Airat R. Kayumov Darya E. Zhuravleva Zalina I. Iskhakova Evgeniy E. Molchanov Dmitriy A. Merkushev Ilya A. Khodov Yuriy S. Marfin 《Molecules (Basel, Switzerland)》2022,27(22)
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. 相似文献
62.
Egor I. Nagaev Ilya V. Baimler Alexey S. Baryshev Maxim E. Astashev Sergey V. Gudkov 《Molecules (Basel, Switzerland)》2022,27(19)
The influence of laser radiation of a typical surgical laser on the physicochemical properties of the Bovine Serum Albumin (BSA) protein was studied. It was established that the physicochemical characteristics of optical breakdown weakly depend on the concentration of protein molecules. At the same time, the patterns observed for an aqueous solution of BSA irradiated with a laser for different time periods were extremely similar to the classical ones. It was established that after exposure to laser radiation, the optical density of protein solutions increases. At the same time, the intensity of BSA fluorescence due to aromatic amino acid residues decreases insignificantly after exposure to laser radiation. In this case, the position of the excitation and emission maximum does not change, and the shape of the fluorescence spot on 3D maps also does not change significantly. On the Raman spectrum after exposure to laser radiation, a significant decrease in 1570 cm−1 was observed, which indicates the degradation of α-helices and, as a result, partial denaturation of BSA molecules. Partial denaturation did not significantly change the total area of protein molecules, since the refractive index of solutions did not change significantly. However, in BSA solutions, after exposure to laser radiation, the viscosity increased, and the pseudoplasticity of aqueous solutions decreased. In this case, there was no massive damage to the polypeptide chain; on the contrary, when exposed to optical breakdown, intense aggregation was observed, while aggregates with a size of 400 nm or more appeared in the solution. Thus, under the action of optical breakdown induced by laser radiation in a BSA solution, the processes of partial denaturation and aggregation prevail, aromatic amino acid residues are damaged to a lesser extent, and fragmentation of protein molecules is not observed. 相似文献
63.
Are there reliable DFT approaches for 13C NMR chemical shift predictions of fullerene C60 derivatives? 下载免费PDF全文
Arthur R. Tulyabaev Ilya I. Kiryanov Ilnaz S. Samigullin Leonard M. Khalilov 《International journal of quantum chemistry》2017,117(1):7-14
The relationships between experimental and theoretical 13C NMR chemical shifts of a pristine fullerene C60, monoadducts from [2 + n] cycloaddition (n = 1–3), and one [2 + 1] bis‐adduct are systematically analyzed for the first time by using diverse quantum‐chemical levels of theory. These levels involved B3LYP, B3PW91, B97‐2, mPW1PW91, PBE1PBE, and X3LYP hybrid functionals combined with 3‐21G, 6‐31G, 6‐31G(d), 6‐31G(d,p), 6‐31G(d,2p), LanL2DZ, and SDDAll basis sets. X3LYP/6‐31G approach is determined to have the lowest deviations from the 13C NMR experimental data compared to the other methods for all the fullerene compounds (mean absolute error value is 0.856 ppm and root mean squared error value is 1.197 ppm). The highest deviations are characteristic for α (sp2 C2/C5/C8/C10) and β (sp2 C6/C7/C11/C12) carbon atoms relative to a functionalization site and for those (sp3 C1/C9) directly attached with a side fragment in the [2 + n] monoadducts (n = 1–3). A probable reason of such deviation is that the approaches do not take into account a contribution of paramagnetic ring currents to 13C NMR chemical shifts. The results will be useful in design of novel fullerene derivatives and in performing unambiguous 13C NMR chemical shift assignments with modern quantum chemistry calculations. 相似文献
64.
P. G. Polishchuk T. I. Madzhidov A. Varnek 《Journal of computer-aided molecular design》2013,27(8):675-679
The goal of this paper is to estimate the number of realistic drug-like molecules which could ever be synthesized. Unlike previous studies based on exhaustive enumeration of molecular graphs or on combinatorial enumeration preselected fragments, we used results of constrained graphs enumeration by Reymond to establish a correlation between the number of generated structures (M) and the number of heavy atoms (N): logM = 0.584 × N × logN + 0.356. The number of atoms limiting drug-like chemical space of molecules which follow Lipinsky’s rules (N = 36) has been obtained from the analysis of the PubChem database. This results in M ≈ 1033 which is in between the numbers estimated by Ertl (1023) and by Bohacek (1060). 相似文献
65.
Ilya V. Mishakov Ekaterina V. Ilyina Alexander F. Bedilo Aleksey A. Vedyagin 《Reaction Kinetics and Catalysis Letters》2009,97(2):355-361
Nanocrystalline aerogel VOx/MgO catalysts for the oxidative dehydrogenation of propane with high surface area and uniform vanadium distribution were
synthesized by co-gelation followed by supercritical drying. The catalysts were shown to have superior performance compared
to nanocrystalline VOx/MgO catalysts prepared by impregnation. 相似文献
66.
A general method has been developed for arylation of readily available 1H-perfluoroalkanes. The method employs aryl iodide and 1H-perfluoroalkane reagents, DMPU solvent, TMP(2)Zn base, and a copper chloride/phenanthroline catalyst. Preliminary mechanistic studies are reported. 相似文献
67.
Gridnev ID Alberico E Gladiali S 《Chemical communications (Cambridge, England)》2012,48(16):2186-2188
The mechanism of asymmetric hydrogenation catalyzed by [Rh(NBD)((R)-PhenylBinepine)(2)]SbF(6)1 has been studied by NMR experiments and DFT computations. Either the low-temperature hydrogenation of the catalyst-substrate adduct 4 or the reaction of solvate dihydride 6 with MAC produced the hydrogenation product with over 99% ee (S). 相似文献
68.
69.
Yuriy A. Zhabanov Alexey V. Eroshin Igor V. Ryzhov Ilya A. Kuzmin Daniil N. Finogenov Pavel A. Stuzhin 《Molecules (Basel, Switzerland)》2021,26(10)
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 D2h and D4h symmetry was obtained for H2TTDPz and NiTTDPz, respectively. According to data obtained by the MCQDPT2 method, the nickel complex possesses the ground state 1A1g, 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. 相似文献
70.
Conventional lattice Boltzmann models for the simulation of fluid dynamics are restricted by an error in the stress tensor that is negligible only for small flow velocity and at a singular value of the temperature. To that end, we propose a unified formulation that restores Galilean invariance and the isotropy of the stress tensor by introducing an extended equilibrium. This modification extends lattice Boltzmann models to simulations with higher values of the flow velocity and can be used at temperatures that are higher than the lattice reference temperature, which enhances computational efficiency by decreasing the number of required time steps. Furthermore, the extended model also remains valid for stretched lattices, which are useful when flow gradients are predominant in one direction. The model is validated by simulations of two- and three-dimensional benchmark problems, including the double shear layer flow, the decay of homogeneous isotropic turbulence, the laminar boundary layer over a flat plate and the turbulent channel flow. 相似文献