Evaluation of the molecular polarizability using the IPPP-CLOPPA-INDO/S method. Application to molecules of biological interest

The IPPP-CLOPPA-INDO/S method is introduced to investigate the static molecular polarizability in macromolecules. As an example of application, the polarizability of phospholipidic compounds, with and without the presence of water molecules has been estimated. The IPPP technique was employed to calculate the polarizability of the polar head and the hydrocarbon chains separately to analyze the feasibility of evaluating the total polarizability of the molecule by addition of these two projected results. INDO/S dipole moments of different fragments of the complex molecule were obtained by means of localized molecular orbitals in order to evaluate the charge transfer in the system.     

Frequency autocorrelation function of stochastically fluctuating fields caused by specific magnetic field inhomogeneities

Signal formation in NMR is due to incoherent dephasing of nuclear spins. Of particular practical importance is the situation of nuclear spins undergoing independent stochastic motion in inhomogeneous local magnetic fields, e.g., created by magnetized objects. Since it was demonstrated recently that the frequency correlation function of nuclear spins can be measured directly, a theoretical analysis of such functions is of interest. Here, we provide a numerically exact analysis of that correlation function for the inhomogeneous fields around two particular geometries: cylinders and spheres. The functional form exhibits three regimes: after an initial transient, there is an algebraic regime with a t(-d/2) time dependence (d being the space dimension), followed by an exponential cutoff due to microscopic system size effects. The main parameter controlling the range of the individual regimes is the volume fraction of the magnetized objects. In addition to our numerical analysis, which is based on eigenfunction expansions, we provide analytical results and approximations based on the generalized moment expansion.     

Backbone and side-chain ordering in a small protein

We investigate the relation between backbone and side-chain ordering in a small protein. For this purpose, we have performed multicanonical simulations of the villin headpiece subdomain HP-36, an often used toy model in protein studies. Concepts of circular statistics are introduced to analyze side-chain fluctuations. In contrast to earlier studies on homopolypeptides [Wei et al., J. Phys. Chem. B 111, 4244 (2007)], we do not find collective effects leading to a separate transition. Rather, side-chain ordering is spread over a wide temperature range. Our results indicate a thermal hierarchy of ordering events, with side-chain ordering appearing at temperatures below the helix-coil transition but above the folding transition. We conjecture that this thermal hierarchy reflects an underlying temporal order, and that side-chain ordering facilitates the search for the correct backbone topology.     

Improving surface quality of polyethylene terephthalate film for large area flexible electronic applications

Lamination is a method utilized to protect flexible electroluminescence device against environmental hazards, such as dust, moisture, and water vapor. The materials are typically joined together using adhesive or cohesion of the materials during the lamination process. Polyethylene terephthalate (PET) is commonly used as the substrate film where electroluminescence patterns are printed. However, PET film has a relatively low surface energy and high contact angle, which would cause relatively weak laminating strength. This paper discusses the use of atmospheric plasma as a surface treatment method to modify PET and laminating films’ interface to improve bonding and laminating quality. Experimental results revealed that atmospheric plasma process reduced the contact angle of both PET and laminating films. Functional groups favoring hydrophilicity were found on the films’ interface after the atmospheric plasma treatment. These effects consequently increased surface energies of both films and favored bonding between the films. The treated films thus had increased laminating strength by approximately six times without compromising the transparency quality.     

Complexity results in graph reconstruction

We investigate the relative complexity of the graph isomorphism problem (GI) and problems related to the reconstruction of a graph from its vertex-deleted or edge-deleted subgraphs (in particular, deck checking (DC) and legitimate deck (LD) problems). We show that these problems are closely related for all amounts c?1 of deletion:

(1)

, , , and .

(2)

For all k?2, and .

(3)

For all k?2, .

(4)

.

(5)

For all k?2, .

For many of these results, even the c=1 case was not previously known.Similar to the definition of reconstruction numbers vrn_∃(G) [F. Harary, M. Plantholt, The graph reconstruction number, J. Graph Theory 9 (1985) 451-454] and ern_∃(G) (see [J. Lauri, R. Scapellato Topics in Graph Automorphism and Reconstruction, London Mathematical Society, Cambridge University Press, Cambridge, 2003, p. 120]), we introduce two new graph parameters, vrn_∀(G) and ern_∀(G), and give an example of a family {G_n}_n?4 of graphs on n vertices for which vrn_∃(G_n)<vrn_∀(G_n). For every k?2 and n?1, we show that there exists a collection of k graphs on (2^k-1+1)n+k vertices with 2ⁿ 1-vertex-preimages, i.e., one has families of graph collections whose number of 1-vertex-preimages is huge relative to the size of the graphs involved.     

Extending the dynamic range of electrochemical sensors using multiple modified electrodes

Multiple electrodes, combined with a chemometric strategy to calibrate the measurement response, have been used for the determination of an analyte across a broader dynamic range than is possible with a single electrode. The model system used for the detection of copper comprised electrodes modified with a self-assembled monolayer. The electrodes were modified with the copper-complexing species (3-mercaptopropionic acid, thioctic acid, and the peptides cysteine and Gly-Gly-His) and copper was determined over concentrations ranging from nanomolar to millimolar using voltammetric analysis. We have demonstrated that by combining the calibration functions from the four electrodes a better estimate (i.e. with smaller variance) of the concentration of the analyte is obtained. Measurement uncertainty is expressed for independently prepared electrodes, which allows the possibility of commercial production and factory calibration. The principles of using multiple electrodes modified with recognition elements with different affinities for the target analyte to extend the dynamic range of sensors is a general one that could be applied to other analytes.     

Biophysical parameters influencing secondary oxidants activation in human serum exposed to singlet oxygen

Singlet oxygen (1O?), produced during photodynamic therapy, deactivates during its interaction with tissues by producing reactive oxygen species (ROS) and peroxides as well as other degradation products. Here we investigated the role of parameters of light delivery, O(2), and temperature on the ROS and peroxides production, secondary to 1O?. A series of simple in vitro experiments has been performed with Rose Bengal (RB) as a 1O? producer, human serum (HS) as a target and dichlorofluorescein (DCFH) as a nonspecific marker, becoming fluorescent when oxidized. The overall secondary production of ROS and peroxides in HS had also been compared to fetal calf serum (FCS) or mice sera. Increasing power but with a same delivered energy decreased secondary ROS and peroxides when increasing power with a same duration for light delivery increased them. Increasing delivered energy increased linearly secondary ROS or peroxides. Delivering O? by bubbling before light delivery increased secondary ROS or peroxides, when Ar decreased them. Delivering gases after light delivery had no influence on secondary ROS or peroxides production. Increasing temperature from 20 to 40 °C increased secondary ROS or peroxides production but freezing after light delivery either before or after measurement had only a mild influence. Secondary ROS or peroxides production was 2 or 4 times lower in HS than in FCS or nude mice sera respectively. PDT seems to consist of two subsequent phases, both linked but developing independently. The intensity of photo-reactions varied with the model, human sera producing less secondary ROS than fetal calf or mouse sera. Search for new sensitizers should consider secondary ROS-induced pathways in addition to 1O? production.     

From molecular to macroscopic engineering: shaping hydrogen-bonded organic nanomaterials

The self‐assembly and self‐organization behavior of chromophoric acetylenic scaffolds bearing 2,6‐bis(acetylamino)pyridine ( 1 , 2 ) or uracyl‐type ( 3 – 9 ) terminal groups has been investigated by photophysical and microscopic methods. Systematic absorption and luminescence studies show that 1 and 2 , thanks to a combination of solvophilic/solvophobic forces and π–π stacking interactions, undergo self‐organization in apolar solvents (i.e., cyclohexane) and form spherical nanoparticles, as evidenced by wide‐field optical microscopy, TEM, and AFM analysis. For the longer molecular module, 2 , a more uniform size distribution is found (80–200 nm) compared to 1 (20–1000 nm). Temperature scans in the range 283–353 K show that the self‐organized nanoparticles are reversibly formed and destroyed, being stable at lower temperatures. Molecular modules 1 and 2 were then thoroughly mixed with the complementary triply hydrogen‐bonding units 3 – 9 . Depending on the specific geometrical structure of 3 – 9 , different nanostructures are evidenced by microscopic investigations. Combination of modules 1 or 2 with 3 , which bears only one terminal uracyl unit, leads to the formation of vesicular structures; instead, when 1 is combined with bis‐uracyl derivative 4 or 5 , a structural evolution from nanoparticles to nanowires is observed. The length of the wires obtained by mixing 1 and 4 or 1 and 5 can be controlled by addition of 3 , which prompts transformation of the wires into shorter rods. The replacement of linear system 5 with the related angular modules 6 and 7 enables formation of helical nanostructures, unambiguously evidenced by AFM. Finally, thermally induced self‐assembly was studied in parallel with modules 8 and 9 , in which the uracyl recognition sites are protected with tert‐butyloxycarbonyl (BOC) groups. This strategy allows further control of the self‐assembly/self‐organization process by temperature, since the BOC group is completely removed on heating. Microscopy studies show that the BOC‐protected ditopic modules 8 self‐assemble and self‐organize with 1 into ordered linear nanostructures, whereas BOC‐protected tritopic system 9 gives rise to extended domains of circular nano‐objects in combination with 1 .     

Virtual and experimental high-throughput screening (HTS) in search of novel inosine 5′-monophosphate dehydrogenase II (IMPDH II) inhibitors

IMPDH (Inosine 5??-monophosphate dehydrogenase) catalyzes a rate-limiting step in the de novo biosynthesis of guanine nucleotides. IMPDH inhibition in sensitive cell types (e.g., lymphocytes) blocks proliferation (by blocking RNA and DNA synthesis as a result of decreased cellular levels of guanine nucleotides). This makes it an interesting target for cancer and autoimmune disorders. Currently available IMPDH inhibitors such as mycophenolic acid (MPA, uncompetitive inhibitor) and nucleoside analogs (e.g., ribavirin, competitive inhibitor after intracellular activation by phosphorylation) have unfavorable tolerability profiles which limit their use. Hence, the quest for novel IMPDH inhibitors continues. In the present study, a ligand-based virtual screening using IMPDH inhibitor pharmacophore models was performed on in-house compound collection. A total of 50,000 virtual hits were selected for primary screen using in vitro IMPDH II inhibition up to 10???M. The list of 2,500 hits (with >70?% inhibition) was further subjected to hit confirmation for the determination of IC₅₀ values. The hits obtained were further clustered using maximum common substructure based formalism resulting in 90 classes and 7 singletons. A thorough inspection of these yielded 7 interesting classes in terms of mini-SAR with IC₅₀ values ranging from 0.163???M to little over 25???M. The average ligand efficiency was found to be 0.3 for the best class. The classes thus discovered represent structurally novel chemotypes which can be taken up for further development.     

Light-activated ruthenium complexes photobind DNA and are cytotoxic in the photodynamic therapy window

Incorporation of biquinoline ligands into Ru(ii) polypyridyl complexes produces light-activated systems that eject a ligand and photobind DNA after irradiation with visible and near-IR light. Structural analysis shows that distortion facilitates the photochemistry, and gel shift and cytotoxicity studies prove the compounds act as anti-cancer photodynamic therapy (PDT) agents in the tissue penetrant region.