Comparing ligand interactions with multiple receptors via serial docking

Standard uses of ligand-receptor docking typically focus on the association of candidate ligands with a single targeted receptor, but actual applications increasingly require comparisons across multiple receptors. This study demonstrates that comparative docking to multiple receptors can help to select homology models for virtual compound screening and to discover ligands that bind to one set of receptors but not to another, potentially similar, set. A serial docking algorithm is furthermore described that reduces the computational costs of such calculations by testing compounds against a series of receptor structures and discarding a compound as soon as it fails to satisfy specified bind/no bind criteria for each receptor. The algorithm also realizes substantial efficiencies by taking advantage of the fact that a ligand typically binds in similar conformations to similar receptors. Thus, once detailed docking has been used to fit a ligand into the first of a series of similar receptors, much less extensive calculations can be used for the remaining structures.     

Solid sampling Fourier transform infrared determination of Mancozeb in pesticide formulations

A series of approaches have been assayed for FTIR determination of Mancozeb in several solid commercial fungicides using different calibration strategies. The simplest procedure was based on the use of the ratio between the absorbance of a characteristic band of Mancozeb and that of a KSCN internal standard measured in the FTIR spectra obtained from KBr pellets. It was employed the quotient between peak height absorbance values at 1525 cm⁻¹ for Mancozeb and 2070 cm⁻¹ for KSCN. In these conditions a precision as relative standard deviation (RSD) of 0.6% and a relative accuracy error of 0.8% (w/w) were found. For complex formulations, containing other compounds with characteristic absorption bands at different wavenumbers than Mancozeb, one of them was used as internal reference being employed the standard addition approach. In this case, the Mancozeb bands at 1525 cm⁻¹ or at 1289 cm⁻¹ were employed, being used the ferrocyanide band at 2075 cm⁻¹ as internal reference. RSD values between 0.7-1.4% and a relative accuracy error of 3% (w/w) were found. A third strategy was based on the use of partial least squares (PLS) calibration. A reference set was prepared mixing Mancozeb, Kaolin, Cymoxanil and KBr, being predicted the Mancozeb concentration in pesticide formulations by using the quotient between absorbance bands of Mancozeb and those of Cymoxanil. In these conditions a relative accuracy error of 0.6% (w/w) and a relative standard deviation of 1.3% were found.     

High yield synthesis and reactivity of a phosphinidene bridged dimolybdenum complex

Protonation of [Mo2Cp2(mu-H)(mu-PHR*)(CO)4] (Cp = eta5-C5H5, R* = 2,4,6-C6H2tBu3) with HBF4.OEt2 gives the hydridophosphinidene complex [Mo2Cp2(mu-H)(mu-PR*)(CO)4]BF4, which is easily deprotonated with H2O to give the known phosphinidene complex [Mo2Cp2(mu-PR*)(CO)4] in 95% yield. Reaction of the latter with I2 gives the unsaturated phosphinidene complex [Mo2Cp2I2(mu-PR*)(CO)2], which exhibits an intermetallic distance of 2.960(2) A. Irradiation of solutions of [Mo2Cp2(mu-PR*)(CO)4] with UV light gives a mixture of the triply bonded [Mo2Cp2(mu-PR*)(mu-CO)2] and the hydridophosphido derivative [Mo2Cp2(mu-H){mu-P(CH2CMe2)C6H2tBu2}(CO)4] as major species. The latter complex results from an intramolecular C-H bond cleavage from a tBu group and has been characterized by spectroscopy and an X-ray study. Irradiation in the presence of HCC(p-tol) results in the insertion of the alkyne into the Mo-P bond to give [Mo2Cp2{mu-eta1:eta2,kappa-C(p-tol)CHPR*}(CO)4] structurally characterized through an X-ray study.     

SOLVENT EFFECTS ON THE TAUTOMERIZATION OF 5′-DEOXYPYRIDOXAL. A PHOTOPHYSICAL STUDY

Abstract— Absorption and fluorescence spectra of 5′-deoxypyridoxal (DPL) in various pure solvents and mixtures were recorded both at room temperature and over the range10–65°C. The areas under the absorption bands were analyzed to obtain the mole fraction (f_N, f_z) of two tautomers (the zwitterionic, Z, and neutral, N, forms) in the ground state. The following spectral parameters were determined from the fluorescence spectra: Stokes shift (Δv), fluorescence quantum yield of the neutral form (Q_N), fluorescence ratio of the neutral to the zwitterionic form (ø_N/ø_Z) and the rate constant of tautomerization (k₁) from Z to N in the excited state. Some of these parameters (f_N, Δv, Q_N, k₁) were found to depend on the proton donor character of the solvent, whereas others (ø_N/ø_Z) depended on its dipole moment. Thus, the absorption and fluorescence spectra of DPL allow one to obtain information on the polarity and the concentration of –OH groups on its environment.     

Site-directed photochemical disruption of the actin cytoskeleton by actin-binding Rose Bengal-conjugates

The in situ light-induced, non-enzymatic digestion of cytoskeletal actin by a xanthene dye conjugated to heavy meromyosin, anti-actin antibodies and/or anti-myosin antibodies is reported. The dye Rose Bengal was conjugated to either anti-actin antibodies, anti-myosin antibodies or heavy meromyosin. Under our experimental conditions, visible light induced the non-enzymatic breakdown of cytoskeletal actin when mammalian tissue culture cells were probed either with Rose Bengal-conjugated anti-actin and/or anti-myosin antibodies. Similar results were obtained when tissue culture cells were probed with Rose Bengal-conjugated heavy meromyosin before irradiation with visible light. The in situ photochemical reaction depended on the presence of actin-binding Rose Bengal-conjugates.     

Copolymerization of ethylene and non-conjugated diene using homogenous catalyst

Ethylene and different amounts of 1,7-octadiene were copolymerized using the metallocene catalyst system ethylidene-bis(fluorenyl) zirconium dichloride and methylaluminoxane (MAO) at both 50 and 90 °C. The catalyst activity has slightly increased with the addition of low amounts of the diene in relation to the homopolymerization of ethylene. The obtained polymers were characterized according to their melting temperature (T_m) and crystallinity degree (x_c) by differential scanning calorimetry (DSC). Weight-average molecular weight (M_w) and polydispersity were determined by gel permeation chromatography (GPC). Diene contents in the copolymer were obtained through the FTIR spectroscopy. The results indicated that at polymerization temperature of 90 °C, crosslinking bonds in the obtained copolymers were low, differently from what was observed at 50 °C. The diene content in the copolymer achieved more than 3 mol% and the comonomer conversion was around 15%. Moreover, the obtained copolymers have M_w around 100,000 and large polydispersity.     

Molecular structure and polarity of the C3NH carbene

Ab initio MP 2/4-31G ** calculations indicate that the most stable form of C₃NH is bent and singlet and that the linear structure corresponds to a maximum. The effect of changing the CNH angle on the total energy is slight, but it is quite pronounced on the molecular polarity. The wider angle tends to increase the polarity of C₃NH. MP 2/4-31G ** calculations predict a difference of polarity between linear and bent structures of 0.8 D.     

Transport properties of alkyltrimethylammonium bromide surfactants in aqueous solutions

Differential mutual diffusion coefficients of n-alkyltrimethylammonium bromides [CH₃(CH₂)_n–1N(CH₃)₃Br, C_nTAB] (n=10, 12, 14, 16) have been measured in aqueous solutions at 298.15 K using a conductimetric cell and an automatic apparatus to follow diffusion. The cell is based on an open-ended capillary, and the technique follows the diffusion process by measuring the resistance of a solution inside the capillaries at various times. The electrical conductances of those solutions have also been measured to calculate the critical micellar concentration (cmc). Thermodynamic analysis of the data suggests that the free ion concentration decreases at concentrations above the cmc, in agreement with theoretical predictions. The obtained values of the micellization parameters were used to model the mutual diffusion coefficients of C_nTAB aqueous solutions.     

Relaxation processes in room temperature ionic liquids: the case of 1-butyl-3-methyl imidazolium hexafluorophosphate

A detailed investigation on the nature of the relaxation processes occurring in a typical room temperature ionic liquid (RTIL), namely, 1-butyl-3-methyl imidazolium hexafluorophosphate ([bmim][PF(6)]), is reported. The study was conducted using both elastic and inelastic neutron scattering over a wide temperature range from 10 to 400 K, accessing the dynamic features of both the liquid and glassy amorphous states. In this study, the inelastic fixed energy scan technique has been applied for the first time to this class of materials. Using this technique, the existence of two relaxation processes below the glass transition and a further diffusive process occurring above the glass-liquid transition are observed. The low temperature processes are associated with methyl group rotation and butyl chain relaxation in the glassy state and have been modeled in terms of two Debye-like, Arrhenius activated processes. The high temperature process has been modeled in terms of a Kohlraush-Williams-Watts relaxation, with a distinct Vogel-Fulcher-Tamman temperature dependence. These results provide novel information that will be useful in rationalizing the observed structural and dynamical behavior of RTILs in the amorphous state.     

Reactions of dimethyldivinylsilane,dimethyldivinyltin and allyltrimethyltin with diethylene (tertiary) phosphine)platinum complexes

The compounds [Pt(C₂H₄)₂(PR₃)] [PR₃ = P-tBu₂Me, P(C₆H₁₁)₃, PPh₃] react dimethyldivinylsilane or dimethyldivinyltin to give chelate complexes [Pt{(CH₂CH)₂MMe₂} (PR₃)] (M = Si or Sn). allyltrimethyltin reacts with various diethylene (tertiary phosphine)platinum compounds with cleavage of the allyl group to afford complexes [Pt(SnMe₃)(η³-C₃H₅)(PR₂)]. The NMR spectra (¹³C, ¹H and ³¹P) of the new compounds have been recorded, and the data are discussed in terms of the structures proposed.