4D-QSAR analysis of a series of antifungal p450 inhibitors and 3D-pharmacophore comparisons as a function of alignment

A training set of 55 antifungal p450 analogue inhibitors was used to construct receptor-independent four-dimensional quantitative structure-activity relationship (RI 4D-QSAR) models. Ten different alignments were used to build the models, and one alignment yields a significantly better model than the other alignments. Two different methodologies were used to measure the similarity of the best 4D-QSAR models of each alignment. One method compares the residual of fit between pairs of models using the cross-correlation coefficient of their residuals of fit as a similarity measure. The other method compares the spatial distributions of the IPE types (3D-pharmacophores) of pairs of 4D-QSAR models from different alignments. Optimum models from several different alignments have nearly the same correlation coefficients, r(2), and cross-validation correlation coefficients, xv-r(2), yet the 3D-pharmacophores of these models are very different from one another. The highest 3D-pharmacophore similarity correlation coefficient between any pair of 4D-QSAR models from the 10 alignments considered is only 0.216. However, the best 4D-QSAR models of each alignment do contain some proximate common pharmacorphore sites. A test set of 10 compounds was used to validate the predictivity of the best 4D-QSAR models of each alignment. The "best" model from the 10 alignments has the highest predictivity. The inferred active sites mapped out by the 4D-QSAR models suggest that hydrogen bond interactions are not prevalent when this class of P450 analogue inhibitors binds to the receptor active site. This feature of the 4D-QSAR models is in agreement with the crystal structure results that indicate no ligand-receptor hydrogen bonds are formed.     

Strain‐Induced Isomerization in One‐Dimensional Metal–Organic Chains

The ability to use mechanical strain to steer chemical reactions creates completely new opportunities for solution‐ and solid‐phase synthesis of functional molecules and materials. However, this strategy is not readily applied in the bottom‐up on‐surface synthesis of well‐defined nanostructures. We report an internal strain‐induced skeletal rearrangement of one‐dimensional (1D) metal–organic chains (MOCs) via a concurrent atom shift and bond cleavage on Cu(111) at room temperature. The process involves Cu‐catalyzed debromination of organic monomers to generate 1,5‐dimethylnaphthalene diradicals that coordinate to Cu adatoms, forming MOCs with both homochiral and heterochiral naphthalene backbone arrangements. Bond‐resolved non‐contact atomic force microscopy imaging combined with density functional theory calculations showed that the relief of substrate‐induced internal strain drives the skeletal rearrangement of MOCs via 1,3‐H shifts and shift of Cu adatoms that enable migration of the monomer backbone toward an energetically favorable registry with the Cu(111) substrate. Our findings on this strain‐induced structural rearrangement in 1D systems will enrich the toolbox for on‐surface synthesis of novel functional materials and quantum nanostructures.     

Excited-state characters and dynamics of [W(CO)(5)(4-cyanopyridine)] and [W(CO)(5)(piperidine)] studied by picosecond time-resolved IR and resonance Raman spectroscopy and DFT calculations: roles of W --> L and W --> CO MLCT and LF excited states revised

The characters, dynamics, and relaxation pathways of low-lying excited states of the complexes [W(CO)(5)L] [L = 4-cyanopyridine (pyCN) and piperidine (pip)] were investigated using theoretical and spectroscopic methods. DFT calculations revealed the delocalized character of chemically and spectroscopicaly relevant molecular orbitals and the presence of a low-lying manifold of CO pi-based unoccupied molecular orbitals. Traditional ligand-field arguments are not applicable. The lowest excited states of [W(CO)(5)(pyCN)] are W --> pyCN MLCT in character. They are closely followed in energy by W --> CO MLCT states. Excitation at 400 or 500 nm populates the (3)MLCT(pyCN) excited state, which was characterized by picosecond time-resolved IR and resonance Raman spectroscopy. Excited-state vibrations were assigned using DFT calculations. The (3)MLCT(pyCN) excited state is initially formed highly excited in low-frequency vibrations which cool with time constants between 1 and 20 ps, depending on the excitation wavelength, solvent, and particular high-frequency nu(CO) or nu(CN) mode. The lowest excited states of [W(CO)(5)(pip)] are W --> CO MLCT, as revealed by TD-DFT interpretation of a nanosecond time-resolved IR spectrum that was measured earlier in a low-temperature glass (Johnson, F. P. A.; George, M. W.; Morrison, S. L.; Turner, J. J. J. Chem. Soc., Chem. Commun. 1995, 391-393). MLCT(CO) excitation involves transfer of electron density from the W atom and, to a lesser extent, the trans CO to the pi orbitals of the four cis CO ligands. Optical excitation into MLCT(CO) transition of either complex in fluid solution triggers femtosecond dissociation of a W-N bond, producing [W(CO)(5)(solvent)]. It is initially vibrationally excited both in nu(CO) and anharmonicaly coupled low-frequency modes. Vibrational cooling occurs with time constants of 16-22 ps while the intramolecular vibrational energy redistribution from the v = 1 nu(CO) modes is much slower, 160-220 ps. No LF excited states have been found for the complexes studied in a spectroscopically relevant range up to 6-7 eV. It follows that spectroscopy, photophysics, and photochemistry of [W(CO)(5)L] and related complexes are well described by an interplay of close-lying MLCT(L) and MLCT(CO) excited states. The high-lying LF states play only an indirect photochemical role by modifying potential energy curves of MLCT(CO) states, making them dissociative.     

Substrate affinities for membrane transport proteins determined by 13C cross-polarization magic-angle spinning nuclear magnetic resonance spectroscopy

We have devised methods in which cross-polarization magic-angle spinning (CP-MAS) solid-state NMR is exploited to measure rigorous parameters for binding of (13)C-labeled substrates to membrane transport proteins. The methods were applied to two proteins from Escherichia coli: a nucleoside transporter, NupC, and a glucuronide transporter, GusB. A substantial signal for the binding of methyl [1-(13)C]-beta-d-glucuronide to GusB overexpressed in native membranes was achieved with a sample that contained as little as 20 nmol of GusB protein. The data were fitted to yield a K(D) value of 4.17 mM for the labeled ligand and 0.42 mM for an unlabeled ligand, p-nitrophenyl beta-d-glucuronide, which displaced the labeled compound. CP-MAS was also used to measure binding of [1'-(13)C]uridine to overexpressed NupC. The spectrum of NupC-enriched membranes containing [1'-(13)C]uridine exhibited a large peak from substrate bound to undefined sites other than the transport site, which obscured the signal from substrate bound to NupC. In a novel application of a cross-polarization/polarization-inversion (CPPI) NMR experiment, the signal from undefined binding was eliminated by use of appropriate inversion pulse lengths. By use of CPPI in a titration experiment, a K(D) value of 2.6 mM was determined for uridine bound to NupC. These approaches are broadly applicable to quantifying binding of substrates, inhibitors, drugs, and antibiotics to numerous membrane proteins.     

Synthesis of 3,7-diiodo-2,6-di(thiophen-2-yl)benzo[1,2-b:4,5-b']difurans: functional building blocks for the design of new conjugated polymers

3,7-Diiodo-2,6-di(thiophen-2-yl)benzo[1,2-b:4,5-b']difurans are efficiently prepared by an iodine-promoted double cyclization. This new heterocyclic core is readily modified by the attachment of alkyl chains for improved solubility. The use of these compounds for the synthesis of new conjugated polymers is also reported.     

“Living” free radical graft copolymers I: Preparation and properties

Polymers substituted with thio groups are useful for the photochemical synthesis of graft copolymers. Such copolymers have been prepared by the initial conversion of backbone polymers containing chlorinated substituents into polymers containing diethyldithiocarbamate (TC), isopropyl xanthate (IX) or mercaptobenzothiazole (BT) functionality. The photochemical reaction of monomers with these products produced graft copolymers. A variety of halogenated polymers were investigated as starting materials for these syntheses, including poly(vinyl chloride), chlorinated polyvinyl chloride), chlorinated polyethylene, chlorobutyl rubber and neoprene. Characteristics of the grafting reactions, including “pseudo-living” behavior and tandem grafting aspects, were investigated. Glass transitions of the grafted polymers were found to vary uniformly with composition for most of the grafted products.     

Monte Carlo simulation of the chain length distribution in pulsed-laser polymerization experiments in microemulsion

The Monte Carlo method has been used for numerically simulating pulsed-laser polymerization (PLP) in microemulsion, in order to establish if a shift from inflection point to peak maximum as the best measure of the propagation rate constant, k_p, will occur theoretically. Termination is assumed to be instantaneous in the simulations as droplet sizes can be very small in microemulsions. From the results of the simulations it is found that instantaneous termination indeed causes the peak maximum to become the best measure of k_p. From these results it can be deduced that in bulk it is not simply the Poisson-broadening that causes the peak maximum to yield an overestimation of k_p. This overestimation is rather caused by the fact that the termination rate is finite leading to an asymmetrical peak in the molecular weight distribution. In combination with broadening this yields the inflection point to be the best measure of k_p in the bulk.     

Double-fold C-H oxygenation of arenes using PyrDipSi: a general and efficient traceless/modifiable silicon-tethered directing group

The efficient Pd-catalyzed double-fold C-H oxygenation of arenes into resorcinols using the newly developed 2-pyrimidyldiisopropylsilyl (PyrDipSi) directing group is described. Its use allows for the sequential introduction of OAc and OPiv groups in a one-pot manner to produce orthogonally protected resorcinol derivatives. The PyrDipSi group is superior to the previously developed 2-pyridyldiisopropylsilyl (PyDipSi) group, as it is efficient for monooxygenation of ortho-substituted arenes. Notably, the PyrDipSi group can be easily installed into arene molecules and can be easily removed or modified after the oxygenation reaction.     

Coordination Polymers. 9. Chelate Polymers Derived from Bisphenolic Complexes and Propylenediamine

Chelate polymers derived from bis(2,4-dihydroxybenzaldehyde)propyl-enediimine M and bis(2,4-dihydroxyacetophenone)propylenediimine M (M = Fe²⁺, Co²⁺, Ni²⁺, Cu²⁺, Zn²⁺) with aromatic acid chlorides were prepared by interfacial polycondensation. Also, chelate polysiloxanes were obtained from the same monomers and α,ω-dichloropolydimethyl-siloxane. The spectral, thermal, magnetic, and electrical properties of the polychelates were studied.