Molecular dynamics simulations of a nucleoside analogue of 1,4-dihydro-4-oxoquinoline-3-carboxylic acid synthesized as a potential antiviral agent: Conformational studies in vacuum and in water

Conformational analysis of nucleosides may have direct applications to the structure–activity relationship (SAR) studies and in the design of new drug candidates. Although conformational analysis may be accessed in many different ways, in this work it was performed using molecular dynamics (MD) simulation in order to study the dynamic behavior of a nucleoside derivative of 1,4-dihydro-4-oxoquinoline-3-carboxylic acid, synthesized by our group as a potential antiviral agent. The MD simulation was carried out during 10 ns in vacuum and in a box of water at two different temperatures (i.e., 300 and 600 K) using the AMBER force field. The in vacuum MD simulation results are in agreement with the crystallographic structure and with the DFT calculations of the nucleoside, revealing the anti conformer as the more stable one. The simulation in water, however, shows that both conformers may exist at 300 K, the temperature of the in vivo and in vitro assays, revealing that both the syn and anti conformers should be considered in a MD simulation study of the inhibitor–enzyme complex. Simulations are also in agreement with the NOE experiment, which shows that the anti conformer is the preferential one in DMSO-d6 solution at 298 K.     

Alkylthio bridged 44 cve triangular platinum clusters: synthesis, oxidation, degradation, ligand substitution, and quantum chemical calculations

Acetylplatinum(II) complexes trans-[Pt(COMe)Cl(L)2] (L = PPh3, 2a; P(4-FC6H4)3, 2b) were found to react with dialkyldisulfides R2S2 (R = Me, Et, Pr, Bu; Pr = n-propyl, Bu = n-butyl), yielding trinuclear 44 cve (cluster valence electrons) platinum clusters [(PtL)3(mu-SR)3]Cl (4). The analogous reaction of 2a-b with Ph2S2 gave SPh bridged dinuclear complexes trans-[{PtCl(L)}2(mu-SPh)2] (5), whereas the addition of Bn2S2 (Bn = benzyl) to 2a ended up in the formation of [{Pt(PPh3)}3(mu3-S)(mu-SBn)3]Cl (6). Theoretical studies based on the AIM theory revealed that type 4 complexes must be regarded as triangular platinum clusters with Pt-Pt bonds whereas complex 6 must be treated as a sulfur capped 48 ve (valence electrons) trinuclear platinum(II) complex without Pt-Pt bonding interactions. Phosphine ligands with a lower donor capability in clusters 4 proved to be subject to substitution by stronger donating monodentate phosphine ligands (L' = PMePh2, PMe2Ph, PBu3) yielding clusters [(PtL')3(mu-SR)3]Cl (9). In case of the reaction of clusters 4 and 9 with PPh2CH2PPh2 (dppm), a fragmentation reaction occurred, and the complexes [(PtL)2(mu-SMe)(mu-dppm)]Cl (12) and [Pt(mu-SMe)2(dppm)] (13) were isolated. Furthermore, oxidation reactions of cluster [{Pt(PPh3)}3(mu-SMe)3]Cl (4a) using halogens (Br2, I2) gave dimeric platinum(II) complexes cis-[{PtX(PPh3)}2(mu-SMe)2] (14, X = Br, I) whereas oxidation reactions using sulfur and selenium afforded chalcogen capped trinuclear 48 ve complexes [{Pt(PPh3)}3(mu3-E)(mu-SMe)3] (15, E = S, Se). All compounds were fully characterized by means of NMR and IR spectroscopy, microanalyses, and ESI mass spectrometry. Furthermore, X-ray diffraction analyses were performed for the triangular cluster 4a, the trinuclear complex 6, as well as for the dinuclear complexes trans-[{Pt(AsPh3)}2(mu-SPh)2] (5c), [{Pt(PPh3)}2(mu-SMe)(mu-dppm)]Cl (12a), and [{{PtBr(PPh3)}2(mu-SMe)2] (14a).     

Predicting adsorption isotherms of low-volatile compounds by temperature programmed desorption: iodine on carbon

Equilibrium adsorption isotherms for low-volatile compounds are extremely difficult to measure. A simple technique using temperature programmed desorption (TPD) is proposed. It is demonstrated that the two parameters needed for constructing the Langmuir isotherm can be derived with data from the TPD technique alone. Thus, the Langmuir isotherms of iodine on AX-21 super-activated carbon were obtained with this technique. A series of TPD experiments for samples with different initial loadings of iodine were carried out by varying the heating rates which resulted in different peak desorption temperatures. The peak desorption temperature decreased as the initial loading was increased because of the re-adsorption effect. The Langmuir constant was derived from kinetic theory with the activation energy for desorption obtained from the experiment. The activation energy for desorption was 12.3 kcal/mol. The Langmuir constants determined by this technique were in comparable order of magnitude to the reported values for iodine on activated carbon. The saturation capacity of AX-21 for iodine could also be determined from the TPD data obtained from samples with different initial loadings. The estimated saturation capacity from the TPD experiment was 2.96 g I(2)/g AX-21, which was close to the experimentally measured saturation capacity of 3.25 g I(2)/g AX-21 for the same system.     

The ring-opening reaction of chromenes: a photochemical mode-dependent transformation

The efficiency of the photochemical ring-opening of chromenes (or benzopyrans) depends on the vibronic transition selected by the chosen excitation wavelength. In the present work, ab initio CASPT2//CASSCF calculations are used to determine the excited-state ring-opening reaction coordinate for 2H-chromene (C) and 2,2-diethyl-2H-chromene (DEC) and provide an explanation for such an unusual mode-dependent behavior. It is shown that excited-state relaxation and decay occur via a multimodal and barrierless (or nearly barrierless) reaction coordinate. In particular, the relaxation out of the Franck-Condon involves a combination of in-plane skeletal stretching and out-of-plane modes, while the second part of the reaction coordinate is dominated exclusively by a different out-of-plane mode. Population of this last mode is shown to be preparatory with respect to both C-O bond breaking and decay via an S(1)/S(0) conical intersection. The observed mode-dependent ring-opening efficiency is explained by showing that the vibrational mode corresponding to the most efficient vibronic transition has the largest projection onto the out-of-plane mode of the reaction coordinate. To support the computationally derived mechanism, we provide experimental evidence that the photochemical ring-opening reaction of 2,2-dimethyl-7,8-benzo(2H)chromene, that similarly to DEC exhibits a mode-dependent photoreaction, has a low ( approximately 1 kcal mol(-1)) activation energy barrier.     

Relaxation dynamics in glycerol-water mixtures: I. Glycerol-rich mixtures

We discuss the relaxation dynamics of glycerol-water mixtures, as studied by dielectric spectroscopy in the frequency range from 1 Hz to 250 MHz and at temperatures between 173 and 323 K. The experimental results obtained for the glycerol-rich mixtures suggest that the main dielectric relaxation process, as well as the so-called high-frequency "excess wing" (EW) and dc conductivity, follow the same temperature dependence. This result indicates that all of these processes are induced by the same molecular origin. A new phenomenological function is proposed to describe the whole dielectric spectrum in the covered frequency range, and some possible mechanisms of dielectric behaviors through the dc conductivity, the main relaxation process, and the EW are discussed.     

Output polarization states of a corner cube reflector irradiated at non-normal incidence

A method has been developed for determining the polarization state of the retro-reflected beam from a corner cube irradiated with an input beam of arbitrary polarization state and of arbitrary tilt angle to the cube. Experimentally, the output beam consists of six distinct beamlets of different polarization states that are focused into six non-overlapping regions in the active area of the detector. The overall polarization state of the beam as measured by the photodetector can thus be represented by the incoherent superposition of the polarization states of the six beamlets. Experiments have been performed that verify the theory for a linearly polarized input beam irradiating the corner cube.     

The materials science X‐ray beamline BL8 at the DELTA storage ring

The hard X‐ray beamline BL8 at the superconducting asymmetric wiggler at the 1.5 GeV Dortmund Electron Accelerator DELTA is described. This beamline is dedicated to X‐ray studies in the spectral range from ～1 keV to ～25 keV photon energy. The monochromator as well as the other optical components of the beamline are optimized accordingly. The endstation comprises a six‐axis diffractometer that is capable of carrying heavy loads related to non‐ambient sample environments such as, for example, ultrahigh‐vacuum systems, high‐pressure cells or liquid‐helium cryostats. X‐ray absorption spectra from several reference compounds illustrate the performance. Besides transmission measurements, fluorescence detection for dilute sample systems as well as surface‐sensitive reflection‐mode experiments have been performed. The results show that high‐quality EXAFS data can be obtained in the quick‐scanning EXAFS mode within a few seconds of acquisition time, enabling time‐resolved in situ experiments using standard beamline equipment that is permanently available. The performance of the new beamline, especially in terms of the photon flux and energy resolution, is competitive with other insertion‐device beamlines worldwide, and several sophisticated experiments including surface‐sensitive EXAFS experiments are feasible.     

Fluctuation theorems and 1/f noise from a simple matrix

Here we present a model for a small system combined with an explicit entropy bath that iscomparably small. The dynamics of the model is defined by a simple matrix, M. Each row ofM corresponds to a macrostate of the system, e.g. net alignment, while the elements in therow represent microstates. The constant number of elements in each row ensures constantentropy, which allows reversible fluctuations, similar to information theory where aconstant number of bits allows reversible computations. Many elements in M come from themicrostates of the system, but many others come from the bath. Bypassing the bath statesyields fluctuations that exhibit standard white noise; whereas with bath states the powerspectral density varies as S(f) ∝ 1 /f overa wide range of frequencies, f. Thus, the explicit entropy bath is the mechanismof 1/f noisein this model. Both forms of the model match Crooks’ fluctuation theorem exactly,indicating that the theorem applies not only to infinite reservoirs, but also tofinite-sized baths. The model is used to analyze measurements of 1/f-like noise from asub-micron tunnel junction.     

VISUAL PIGMENTS—10. SPECTROSCOPY AND PHOTOPHYSICAL DYNAMICS OF RETINOL AND RETINYL ETHER

Abstract— The absorption and emission spectra, lifetimes and quantum yields of all-trans retinol have been examined as a function of solvent and temperature. In addition, the spectroscopy of retinyl ether and 2 other polyene alcohols have been determined. Based on the results obtained, we conclude that the singlet excited state of retinol and retinyl cther is of a forbidden character and of the type loosely called ¹A^-_g. Retinol forms a dimer in an alkane solvent when cooling from 298 to 77 K. A general structure for the dimer is proposed.