Simulation of time-resolved vibronic spectra and the possibility of analyzing molecules with similar spectral properties

The possibility of using time-resolved vibronic spectroscopy for spectral analysis of mixtures of chemical compounds with similar optical properties, when traditional methods (based on stedy-state spectra) are inefficient, is demonstrated by using the method of computer simulation. The analysis is carried out by the example of molecules of a series of polyenes (butadiene, hexadiene, octatetraene, decapentaene, and decatetraene), their various cis-and trans-rotational isomers, and phenyl-substituted polyenes. Ranges of relative concentrations of molecules similar in their spectral properties, where reliable interpretation of time-resolved spectra of mixtures and both qualitative and quantitative analyses are possible, are determined. The use of computer simulation methods for optimizing full-scale experiments in femtosecond spectroscopy is shown to hold much promise.     

Ab initio calculations of vibronic activity in phosphorescence microwave double resonance spectra of p-dichlorobenzene

The phosphorescence spectrum of p-dichlorobenzene has been calculated using multiconfiguration self-consistent-field wave functions and the quadratic response technique. Attention has been paid to the intensity distribution of the singlet–triplet (³B_1u¹A_g) transition through a number of vibronic subbands. The second order spin–orbit coupling (SOC) contribution to the spin splitting of the ³B_1u (^3*) state is found to be almost negligible, and the calculations therefore provide a good estimate for the zero-field splitting (ZFS) parameters based only on the electron spin–spin coupling expectation values. Nuclear quadrupole resonance constants for the different Cl isotopes are also calculated to accomplish the ZFS assignment. The electric dipole activity of the spin sublevels in the triplet–singlet transitions to the ground-state vibrational levels is estimated by calculations of derivatives using distorted geometries which are shifted from the equilibrium position along different vibrational modes. A vibrational analysis of the phosphorescence spectrum, based on the SOC-induced mixing of the singlet and triplet states calculated along different vibrational modes, provides reasonable agreement with experimental data.Acknowledgment O. R.-P. would like to thank the European MOLPROP network for support. The authors thank Alexander Baev for fruitful discussions. This work was supported by the Swedish Royal Academy of Science (KVA).     

Crystal and molecular structure of nitraminotetrazole and nitramino-1,2,4-triazole. IV. 5-nitraminotetrazole sodium salt sesquihydrate

The structure of 5-nitraminotetrazole sodium salt sesquihydrate was determined by X-ray diffraction. The crystals are monoclinic, space group P2₁/c;a = 3.551(1) Å, b = 21.834(4) Å, c = 9.075(2) Å; = 110.68(3)°; V = 658.3(2) ų; Z = 4; _calc = 1.807 g/cm³. The anion is planar and has an intramolecular hydrogen bond. The negative charge of the anion is localized on one of the oxygens of the nitro group. The sodium cation (c.n.6) is coordinated by three oxygen atoms of different anions and three oxygens of crystallization water. One of the crystallization water molecules is disordered in the unit cell. The anions are hydrogen-bonded with each other and with crystallization water molecules.Original Russian Text Copyright © 2004 by A. M. Astakhov, A. D. Vasiliev, M. S. Molokeev, L. A. Kruglyakova, A. M. Sirotinin, and R. S. StepanovTranslated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 3, pp. 562–565, May–June 2004.     

Modified AutoDock for accurate docking of protein kinase inhibitors

Protein kinases are an important class of enzymes controlling virtually all cellular signaling pathways. Consequently, selective inhibitors of protein kinases have attracted significant interest as potential new drugs for many diseases. Computational methods, including molecular docking, have increasingly been used in the inhibitor design process [1]. We have considered several docking packages in order to strengthen our kinase inhibitor work with computational capabilities. In our experience, AutoDock offered a reasonable combination of accuracy and speed, as opposed to methods that specialize either in fast database searches or detailed and computationally intensive calculations.However, AutoDock did not perform well in cases where extensive hydrophobic contacts were involved, such as docking of SB203580 to its target protein kinase p38. Another shortcoming was a hydrogen bonding energy function, which underestimated the attraction component and, thus, did not allow for sufficiently accurate modeling of the key hydrogen bonds in the kinase-inhibitor complexes.We have modified the parameter set used to model hydrogen bonds, which increased the accuracy of AutoDock and appeared to be generally applicable to many kinase-inhibitor pairs without customization. Binding to largely hydrophobic sites, such as the active site of p38, was significantly improved by introducing a correction factor selectively affecting only carbon and hydrogen energy grids, thus, providing an effective, although approximate, treatment of solvation.     

Pimprinols A–C,from the terrestrial actinomycete,Streptomyces sp.

A Streptomyces sp. Lv3-13, isolated from the rhizosphere soil of the plant Mespilus germanica, has yielded three new pimprinine derivatives, named pimprinols A–C (1–3) and the unknown (2-aminophenyl)(2-ethyloxazol-5-yl) methanone (4) along with the known compounds 2-ethyl oxazole pimprinine and 2-propyl oxazole pimprinine. The structures of the compounds were elucidated based on spectroscopic methods including UV, HR-ESIMS and 1D, 2D NMR data. Compounds 1–4 were screened for antimicrobial and cytotoxic activities.     

The influence of Au-nanoparticles presence in PDMS on microstructures creation by ion beam lithography

3D microstructures in pure poly(dimethylsiloxane) (PDMS) and PDMS with embedded Au nanoparticles were prepared by ion beam lithography without any further etching. Two mega-electron volts helium and 10 MeV oxygen ions were used for ion microstructuring. Parallel lines of 1 mm in length and 10 μm in thickness were fabricated for investigation of the effect of the nanoparticles presence in the polymer on the surface morphology of the created microstructures. The created microstructures were checked by optical microscope. Infrared (IR) spectrometry was used to study the effect of the ions type and fluence on the chemical changes of the material. Atomic force microscopy was used for the fine detail study as well as for checking the microstructure quality. Analysis revealed an increased radiation resistance of the nanocomposite compared to the pure PDMS. Shrinkage is proportional to the fluence, but the maximum value for both materials is limited by saturation. 3D microstructure in modified PDMS obtained at the same irradiation condition as pure PDMS is characterized by its smaller height. Obtaining the microstructure in nanocomposite of the same height as in pure PDMS by increasing the fluence can be impossible due to saturation of shrinkage and/or radiation-induced heating of the material.     

Electron Transport in Configurational Model of Ferromagnetic Fulleride with Triple Orbital Degeneracy

Abstract

Phenomenon of ferromagnetic ordering was for a long time associated exclusively with transition metal and rare-earth compounds. Nowadays this view is challenged by growing evidence that in molecular carbon-based systems the ferromagnetic alignment of spins can be observed as well. We have developed a microscopical model of a fulleride electronic subsystem taking into account triple orbital degeneracy of energy states within the configurational-operator approach. Using the Green function method the energy spectrum of the model has been calculated. Conditions for the ferromagnetic state stabilization have been determined. Static electrical conductivity and effective masses of current carriers in the system with orbitally degenerated energy band have been obtained. In the ground state and for low temperatures at different forms of unperturbed density of electronic states the concentration dependences of transport characteristics for less-then-half-filled lower quasiparticle subband have been calculated.     

Desynchronization transitions in nonlinearly coupled phase oscillators

We consider the nonlinear extension of the Kuramoto model of globally coupled phase oscillators where the phase shift in the coupling function depends on the order parameter. A bifurcation analysis of the transition from fully synchronous state to partial synchrony is performed. We demonstrate that for small ensembles it is typically mediated by stable cluster states, that disappear with creation of heteroclinic cycles, while for a larger number of oscillators a direct transition from full synchrony to a periodic or a quasiperiodic regime occurs.