DNA modified with metal complexes: Applications in the construction of higher order metal–DNA nanostructures

DNA has recently emerged as a useful building block for higher order nanostructures, such as extended two-dimensional surfaces and discrete two- and three-dimensional structures. Transition metal complexes can introduce functionality to these otherwise passive nanostructures. This review examines the synthetic strategies used to introduce metals in a site-specific manner to DNA: either by attaching preformed metal complexes to DNA, or by metal coordination to unmodified or modified DNA. The applications of metal–DNA complexes in building higher order nanostructures and the utility of attaching luminescent or electrochemical labels are discussed.     

High‐Resolution Structural Characterization of a Helical α/β‐Peptide Foldamer Bound to the Anti‐Apoptotic Protein Bcl‐xL

Get into the groove : The first high‐resolution structure of a foldamer bound to a protein target is described (see picture; foldamer in sticks). The foldamer consists of α‐ and β‐amino acid residues and is bound to the anti‐apoptotic protein Bcl‐x_L. The overall binding mode and key interactions observed in the foldamer/Bcl‐x_L complex mimic those seen in complexes of Bcl‐x_L with natural α‐peptide ligands. Additional contacts in the foldamer/Bcl‐x_L complex involving β‐amino acid residues appear to contribute to binding affinity.

     

Determination of lipid phase transition temperatures in hybrid bilayer membranes

The main gel-to-liquid-crystal (LC) phase transition temperature, T(m), of the lipid monolayer in hybrid bilayer membranes (HBMs) was investigated using vibrational sum frequency spectroscopy (VSFS). In the gel phase, the acyl chains of the lipid molecules assume an ordered, all-trans configuration, whereas in the LC phase, the acyl chains exhibit a significant number of disordered gauche conformers. VSFS has unique sensitivity to the order/disorder transitions in the acyl chains and was used to determine T(m) for a series of saturated phosphatidylcholine lipids on octadecanethiolate self-assembled monolayers (SAMs). The values obtained for T(m) for all lipids studied are significantly higher than for the corresponding lipids in vesicles in solution. Additionally, the transition widths are broader for the lipids in HBMs. The underlying SAM clearly influences the phase behavior of the overlying lipid monolayer.     

Strain estimates for small-ring cyclic allenes and butatrienes

Isodesmic and homodesmic equations at the B3LYP/6-311+G(d,p)+ZPVE level of theory have been used to estimate strain for the homologous series of cyclic allenes and cyclic butatrienes. A simple fragment deformation approach also has been applied and appears to work better for the larger rings. For the cyclic allene series, estimates for allene functional group strain (kcal/mol) include: 1,2-cyclobutadiene, 65; 1,2-cyclopentadiene, 51; 1,2-cyclohexadiene, 32; 1,2-cycloheptadiene, 14; 1,2-cyclooctadiene, 5; 1,2-cyclononadiene, 2; 1,2,4-cyclohexatriene, 34; and bicyclo[3.2.1]octa-2,3-diene, 39. For cyclic butatrienes, functional group strain estimates include: 1,2,3-cyclobutatriene, >100; 1,2,3-cyclopentatriene, 80; 1,2,3-cyclohexatriene, 50; 1,2,3-cycloheptatriene, 26; 1,2,3-cyclooctatriene, 17; and 1,2,3-cyclononatriene, 4. Barriers to interconversion of enantiomers in cyclic allenes are reduced with increasing strain. Newly predicted values include: 1,2-cyclopentadiene <1 kcal/mol and bicyclo[3.2.1]octa-2,3-diene, 7.4 kcal/mol. Estimated levels of strain parallel the known reactivity of these substances.     

Photoacoustic infrared spectroscopy of Syncrude post-extraction oil sand

Rapid- and step-scan photoacoustic (PA) infrared spectra of three fractions of a Syncrude post-extraction oil sand were analyzed in detail in this work. The rapid-scan spectra showed that the samples were comprised primarily of kaolinite, quartz, silica, siderite, and residual hydrocarbons, and that the proportions of these constituents were different for each fraction. Depth profiling of the three post-extraction oil sands was accomplished using both rapid- and step-scan PA infrared spectroscopy. The results confirmed that kaolinite is more abundant in the near-surface region, whereas quartz and hydrocarbons are concentrated at greater depths. The modulation frequency dependence of the PA intensities for all three fractions was consistent with a model in which the samples are thermally thick; in other words, the thermal diffusion length (roughly equal to the sampling depth) was less than the particle sizes of all three samples. The results of this study are consistent with published reports on the PA infrared spectra of fine tailings generated during bitumen extraction and the spectroscopic and thermophysical characterization of clay soils and an appropriate model clay.     

Experimental and density functional theoretical investigations of linkage isomerism in six-coordinate FeNO(6) iron porphyrins with axial nitrosyl and nitro ligands

A critical component of the biological activity of NO and nitrite involves their coordination to the iron center in heme proteins. Irradiation (330 < lambda < 500 nm) of the nitrosyl-nitro compound (TPP)Fe(NO)(NO(2)) (TPP = tetraphenylporphyrinato dianion) at 11 K results in changes in the IR spectrum associated with both nitro-to-nitrito and nitrosyl-to-isonitrosyl linkage isomerism. Only the nitro-to-nitrito linkage isomer is obtained at 200 K, indicating that the isonitrosyl linkage isomer is less stable than the nitrito linkage isomer. DFT calculations reveal two ground-state conformations of (porphine)Fe(NO)(NO(2)) that differ in the relative axial ligand orientations (i.e., GS parallel and GS perpendicular). In both conformations, the FeNO group is bent (156.4 degrees for GS parallel, 159.8 degrees for GS perpendicular) for this formally {FeNO}(6) compound. Three conformations of the nitrosyl-nitrito isomer (porphine)Fe(NO)(ONO) (MSa parallel, MSa perpendicular, and MSa(L)) and two conformations of the isonitrosyl-nitro isomer (porphine)Fe(ON)(NO(2)) (MSb parallel and MSb perpendicular) are identified, as are three conformations of the double-linkage isomer (porphine)Fe(ON)(ONO) (MSc parallel, MSc perpendicular, MSc(L)). Only 2 of the 10 optimized geometries contain near-linear FeNO (MSa(L)) and FeON (MSc(L)) bonds. The energies of the ground-state and isomeric structures increase in the order GS < MSa < MSb < MSc. Vibrational frequencies for all of the linkage isomers have been calculated, and the theoretical gas-phase absorption spectrum of (porphine)Fe(NO)(NO(2)) has been analyzed to obtain information on the electronic transitions responsible for the linkage isomerization. Comparison of the experimental and theoretical IR spectra does not provide evidence for the existence of a double linkage isomer of (TPP)Fe(NO)(NO(2)).     

Antiparallel-aligned neutral-ground-state and zwitterionic chromophores as a nonlinear optical material

Efficient noncentrosymmetric arrangement of nonlinear optical (NLO) chromophores with high first-order hyperpolarizability (beta) for increased electro-optical (EO) efficiency has proven challenging as strong dipolar interactions between the chromophores encourage antiparallel alignment, attenuating the macroscopic EO effect. This work explores a novel approach to simultaneously achieve large beta values while providing an adjustable dipole moment by linking a strong neutral-ground-state (NGS) NLO chromophore with positive beta to a zwitterionic (ZWI) chromophore with negative beta in an antiparallel fashion. It is proposed that the overall beta of such a structure will be the sum of the absolute values of the two types of chromophores while the dipole moment will be the difference. Molecules 1-3 were synthesized to test the feasibility of this approach. Molecular dynamics calculations and NMR data supported that the NGS chromophore component and the ZWI chromophore component self-assemble to an antiparallel conformation in chloroform. Calculations showed that the dipole moment of 1 is close to the difference of the two component chromophores. Hyper-Rayleigh scattering (HRS) studies confirmed that the first hyperpolarizability of 1 is close to the sum of the two component chromophores. These results support the idea that an antiparallel-aligned neutral-ground-state chromophore and a zwitterionic chromophore can simultaneously achieve an increase in beta and a decrease of the dipole moment.     

A structure-based 3D-QSAR study of anthrapyrazole analogues of the anticancer agents losoxantrone and piroxantrone

A series of 13 anthrapyrazole compounds that are analogues of piroxantrone and losoxantrone were synthesized, and their cell growth inhibitory effects, DNA binding, topoisomerase IIalpha mediated (EC 5.99.1.3) cleavage of DNA, and inhibition of DNA topoisomerase IIalpha decatenation catalytic activities were determined. Cell growth inhibitory activity was well-correlated with DNA binding, suggesting that these compounds may act by targeting DNA. However, cell growth inhibition was not well-correlated with the inhibition of topoisomerase IIalpha catalytic activity, suggesting that these anthrapyrazoles did not act solely by inhibiting the catalytic activity of topoisomerase II. Most of the analogues were able to induce DNA cleavage, and thus, it was concluded that they acted, at least in part, as topoisomerase II poisons. Structure-based three-dimensional quantitative structure-activity analyses (3D-QSAR) were carried out on the aligned structures of the anthrapyrazoles docked into DNA using comparative molecular field analysis (CoMFA) and comparative molecular similarity index (CoMSIA) analyses in order to determine the structural features responsible for their activity. Both CoMFA and CoMSIA yielded statistically significant models upon partial least-squares analyses. The 3D-QSAR analyses showed that hydrogen-bond donor interactions and electrostatic interactions with the protonated amino side chains of the anthrapyrazoles led to high cell growth inhibitory activity.     

Developing teacher content understanding by integrating pH and logarithms concepts

Logarithms are notorious for being a difficult concept to understand and teach. Research suggests that learners can be supported in understanding logarithms by making connections between mathematics and science concepts such as pH. This study investigated how an integrated chemistry and mathematics lesson impacted 29 teachers’ understanding of the logarithmic relationship and pH. Pre- and post-test data indicated 23 teachers improved their understanding of logarithms and 28 improved their understanding of pH, suggesting that teacher educators in both science and mathematics context can use this approach to foster better understanding with their teachers and ultimately school students. Our analysis also identified professional development components and teacher characteristics associated with gains in understanding of pH and logarithms, which mathematics and science teacher educators can use to strategically adapt and implement the lesson within other teacher education settings.     

Random fluctuations of convex domains and lattice points

In this paper, we examine a random version of the lattice point problem. Let denote the class of all homogeneous functions in of degree one, positive away from the origin. Let be a random element of , defined on probability space , and define

for . We prove that, if , where , then

where , the expected volume. That is, on average, . We give explicit examples in which the Gaussian curvature of is small with high probability, and the estimate holds nevertheless.