Ambient stable solution-processed organic field effect transistors from electron deficient planar aromatics: effect of end-groups on ambient stability.

Ambient stable solution processed n-channel organic field effect transistors (OFETs) are essential for next-generation low-cost organic electronic devices. Several molecular features, such as suitable orbital energy levels, easy synthetic steps, etc., must be considered while designing efficient active layer materials. Here, we report a case of improved ambient stability of solution-processed n-type OFETs upon suitable end-groups substitution of the active layer materials. A pair of core-substituted napthalenediimide (NDIFCN2 and EHNDICN2) derivatives with alkyl and perfluorinated end groups are considered. The transistor devices made out of these two derivatives exhibited largely different ambient stability behavior. The superior device stability (more than 25 days under ambient conditions) of one of the derivatives (NDIFCN2) was ascribed to the presence of fluorinated end groups that function as hydrophobic guard units inhibiting moisture infiltration into the active layer, thereby achieving ambient stability under humid conditions (>65% relative atmospheric humidity). Molecular level optical and electrochemical properties, thermal stability, and the solution-processed (spin coat and drop cast active layers) device characteristics are described in detail. Our findings highlight the requirement of hydrophobic end groups or sidechains for ambient stability of active layer materials, along with deep LUMO levels for ambient stability.

Crystallizing Sub 10 nm Covalent Organic Framework Thin Films via Interfacial-Residual Concomitance.

Synthesis of covalent organic framework (COF) thin films on different supports with high crystallinity and porosity is crucial for their potential applications. We have designed a new synchronized methodology, residual crystallization (RC), to synthesize sub 10 nm COF thin films. These residual crystallized COF thin films showcase high surface area, crystallinity, and conductivity at room temperature. We have used interfacial crystallization (IC) as a rate-controlling tool for simultaneous residual crystallization. We have also diversified the methodology of residual crystallization by utilizing two different crystallization pathways: fiber-to-film (F-F) and sphere-to-film (S-F). In both cases, we could obtain continuous COF thin films with high crystallinity and porosity grown on various substrates (the highest surface area of a TpAzo COF thin film being 2093 m2 g-1). Precise control over the crystallization allows the synthesis of macroscopic defect-free sub 10 nm COF thin films with a minimum thickness of ∼1.8 nm. We have synthesized two COF thin films (TpAzo and TpDPP) using F-F and S-F pathways on different supports such as borosilicate glass, FTO, silicon, Cu, metal, and ITO. Also, we have investigated the mechanism of the growth of these thin films on various substrates with different wettability. Further, a hydrophilic support (glass) was used to grow the thin films in situ for four-probe system device fabrication. All residual crystallized COF thin films exhibit outstanding conductivity values. We could obtain a conductivity of 3.7 × 10-2 mS cm-1 for the TpAzo film synthesized by S-F residual crystallization.

Incorporating a redox active entity to attain electrical bistability in a polymer semiconductor.

Owing to the advantages of 3-D printable stack, scalability and low cost solution state production, polymer-based resistive memory devices have been identified as the promising alternative for conventional oxide technology. Resistive memory devices based on the redox switch mechanism is particularly found to yield high precision with respect to the operational voltages. Reversible non-volatile resistive state switching was realized with high device yield (>80%), with a redox-active chemical entity conjugated to the polymeric semiconductor, and the control experiments with the model compound confirmed the imperative role of the redox-active anthraquinone center in the polymeric backbone. Highly uniform nanodomains and the trap free layers excluded the possibilities of other known switching mechanisms. Optical studies and the molecular modelling data assert the presence of strong charge transfer characteristics upon optical excitation due to the insertion of the anthraquinone unit, which was detrimental in exhibiting bistable conductive states in electrical bias as well.

Influence of non-covalent interactions in dictating the polarity and mobility of charge carriers in a series of crystalline NDIs: a computational case study.

Polycyclic aromatic compounds and their derivatives have emerged as potential molecular entities for air-stable n-type organic semiconductors. In particular, naphthalene diimide (NDI)-derived compounds stand out as one of the most promising classes of molecules that have been studied extensively. There have been a lot of debatable experimental reports on the OFET performance characteristics of some of these materials, which have not yet been resolved completely. Hence, the critical intrinsic aspect of the molecular materials during charge transport in a bulk crystalline state would be essential to categorise the potential candidates. As a case study, in this comprehensive computational approach, we investigated the structural and supramolecular organization in single crystals and the role of those aspects in the bulk carrier transport of a group of selected end-substituted NDI derivatives. A subtle alteration of the end group was observed to result in the modulation of the polarity of charge transport and the charge carrier mobility in the single crystalline state. The disparity is addressed by considering the electronic coupling of the transport states, symmetry of the frontier molecular orbitals and various non-covalent intermolecular interactions. We expect that the present study would benefit towards the rational designing of air-stable n-type organic molecular semiconductors for efficient electronic devices.

Structural alteration of low pH, low temperature induced protonated form of DNA to the canonical form by the benzophenanthridine alkaloid nitidine: Spectroscopic exploration.

Polymorphism of DNA plays a very important part of research relating to the drug-DNA interactions. Here main focus of our investigation is to monitor the interaction of the benzophenanthridine plant alkaloid, nitidine (NIT) with two different forms of DNA i.e. B-DNA and protonated form of DNA maintaining proper temperatures and buffer conditions. Binding interaction of NIT was ascertained from the UV-Visible spectroscopic and spectrofluorimetric titration experiments. Binding constants of the interactions of NIT with different polymorphic forms were calculated from UV-absorption study. The binding constants were 3.8 × 105 M-1 and 1.3 × 105 M-1 for B-DNA and protonated DNA respectively. Red shift in the absorption maxima of NIT on binding with DNA, comparatively greater relative quenching of fluorescence intensity of free NIT than bound NIT, perturbation in the CD spectrum of DNA in presence of NIT confirmed the mode of binding as intercalation. Moreover, spectropolarimetric experiment confirms that left handed protonated form of DNA gets partially converted to the canonical B form of DNA while binds with NIT. Besides the CD experiment, thermal melting experiment also showed that on binding with NIT stabilization of protonated DNA was increased to an appreciable extent.

Molecular mapping and functional characterization of the VEGF164 heparin-binding domain.

The longer splice isoforms of vascular endothelial growth factor-A (VEGF-A), including mouse VEGF164, contain a highly basic heparin-binding domain (HBD), which imparts the ability of these isoforms to be deposited in the heparan sulfate-rich extracellular matrix and to interact with the prototype sulfated glycosaminoglycan, heparin. The shortest isoform, VEGF120, lacks this highly basic domain and is freely diffusible upon secretion. Although the HBD has been attributed significant relevance to VEGF-A biology, the molecular determinants of the heparin-binding site are unknown. We used site-directed mutagenesis to identify amino acid residues that are critical for heparin binding activity of the VEGF164 HBD. We focused on basic residues and found Arg-13, Arg-14, and Arg-49 to be critical for heparin binding and interaction with extracellular matrix in tissue samples. We also examined the cellular and biochemical consequences of abolishing heparin-binding function, measuring the ability of the mutants to interact with VEGF receptors, induce endothelial cell gene expression, and trigger microvessel outgrowth. Induction of tissue factor expression, vessel outgrowth, and binding to VEGFR2 were unaffected by the HBD mutations. In contrast, the HBD mutants showed slightly decreased binding to the NRP1 (neuropilin-1) receptor, and analyses suggested the heparin and NRP1 binding sites to be distinct but overlapping. Finally, mutations that affect the heparin binding activity also led to an unexpected reduction in the affinity of VEGF164 binding specifically to VEGFR1. This finding provides a potential basis for previous observations suggesting enhanced potency of VEGF164 versus VEGF120 in VEGFR1-mediated signaling in inflammatory cells.

Conformational screening of oligonucleotides by variable-temperature high performance liquid chromatography: dissecting the duplex-hairpin-coil equilibria of d(CGCGAATTCGCG).

This study probes the potential of variable-temperature high performance liquid chromatography (VT-HPLC) as a tool for dissecting and modulating nucleic acid structural transitions, using as a model the duplex-hairpin-coil transitions of d(CGCGAATTCGCG). It is demonstrated that VT-HPLC, combined with diode-array detection of the uv signal, enables, for the first time, a physical separation of spectroscopically distinct species that can be assigned to the duplex, hairpin, and coil forms of d(CGCGAATTCGCG). Although the species are spectroscopically distinguishable, they are not readily isolated. Hence, if fractions from the peaks for hairpin or duplex forms are collected and subsequently reinjected onto the cartridge, reequilibration occurs, and both hairpin and duplex peaks are observed. Area integration of the peaks corresponding to duplex and hairpin species provides a means to monitor the duplex to hairpin transition at effective concentrations in the nanomolar range, well below that accessible by conventional spectrophotometers. Concentration-dependent equilibrium constants, melting temperatures, and standard state enthalpies extracted from our measurements compare very well with previous literature results, and with our own results that take into account the effect of our solvent conditions [100 mM TEAA (triethylammonium acetate) and variable acetonitrile] on the melting behavior. By combining precise temperature control with separation based on size, physical behavior, and interaction free energies, VT-HPLC provides a powerful tool for both the modulation and the separation of nucleic acid conformations.

Wobble dC.dA pairing 5' to the cationic guanine N7 8,9-dihydro-8-(N7-guanyl)-9-hydroxyaflatoxin B1 adduct: implications for nontargeted AFB1 mutagenesis.

The structure of 5'-d(ACATC(AFB)GATCT)-3'.5'-d(AGATCAATGT)-3', containing the C(5).A(16) mismatch at the base pair 5' to the modified (AFB)G(6), was determined by NMR. The characteristic 5'-intercalation of the AFB(1) moiety was maintained. The mismatched C(5).A(16) pair existed in the wobble conformation, with the C(5) imino nitrogen hydrogen bonded to the A(16) exocyclic amino group. The wobble pair existed as a mixture of protonated and nonprotonated species. The pK(a) for protonation at the A(16) imino nitrogen was similar to that of the C(5).A(16) wobble pair in the corresponding duplex not adducted with AFB(1). Overall, the presence of AFB(1) did not interfere with wobble pair formation at the mismatched site. Molecular dynamics calculations restrained by distances derived from NOE data and torsion angles derived from (1)H (3)J couplings were carried out for both the protonated and nonprotonated wobble pairs at C(5).A(16). Both sets of calculations predicted the A(16) amino group was within 3 A of the C(5) imino nitrogen. The calculations suggested that protonation of the C(5).A(16) wobble pair should shift C(5) toward the major groove and shift A(16) toward the minor groove. The NMR data showed evidence for the presence of a minor conformation characterized by unusual NOEs between T(4) and (AFB)G(6). T(4) is two nucleotides in the 5'-direction from the modified base. These NOEs suggested that in the minor conformation nucleotide T(4) was in closer proximity to (AFB)G(6) than would be expected for duplex DNA. Modeling studies examined the possibility that T(4) transiently paired with the mismatched A(16), allowing it to come within NOE distance of (AFB)G(6). This model structure was consistent with the unusual NOEs associated with the minor conformation. The structural studies are discussed in relationship to nontargeted C --> T transitions observed 5' to the modified (AFB)G in site-specific mutagenesis experiments [Bailey, E. A., Iyer, R. S., Stone, M. P., Harris, T. M., and Essigmann, J. M. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 1535-1539].

Thermal stabilization of the DNA duplex by adducts of aflatoxin B1.

The trans-8,9-dihydro-8-(N7-guanyl)-9-hydroxyaflatoxin B(1) cationic guanine N7 adduct of aflatoxin B(1) thermally stabilizes the DNA duplex, as reflected in increased T(m) values upon adduction. The magnitude of the increased T(m) value is characteristically 2-3 degrees C. The major rotamer of the neutral guanine N7 adduct trans-8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxy aflatoxin B(1) (the FAPY major adduct) exhibits a 15 degrees C increase in T(m) in 5'-d(CTAT(FAPY)GATTCA)-3'-5'-d(TGAATCATAG)-3'. Site-specific mutagenesis experiments reveal the FAPY major adduct induces G-->T mutations in Escherichia coli at a frequency six times higher than that of the cationic adduct (Smela, M. E.; Hamm, M. L.; Henderson, P. T.; Harris, C. M.; Harris, T. M.; Essigmann, J. M. Proc Natl Acad Sci USA, 99, 6655-6660). Thus, the FAPY major lesion may account substantially for the genotoxicity of AFB(1). Structural studies for cationic and FAPY adducts of aflatoxin B(1) suggest both adducts intercalate above the 5'-face of the modified deoxyguanosine and that in each instance the aflatoxin moiety spans the DNA helix. Intercalation of the aflatoxin moiety, accompanied by favorable stacking with the neighboring base pairs, is thought to account for the increased thermal stability of the aflatoxin cationic guanine N7 and the FAPY major adducts. However, the structural basis for the large increase in thermal stability of the FAPY major adduct in comparison to the cationic guanine N7 adduct of aflatoxin B(1) is not well understood. In light of the site-specific mutagenesis studies, it is of considerable interest. For both adducts, the intercalation structures are similar, although improved stacking with neighboring base pairs is observed for the FAPY major adduct. In addition, the presence of the formamido group in the aflatoxin B(1) FAPY major adduct may enhance duplex stability, perhaps via intrastrand sequence-specific hydrogen bonding interactions within the duplex.

Structural refinement of the 8,9-dihydro-8-(N7-guanyl)-9-hydroxy-aflatoxin B(1) adduct in a 5'-Cp(AFB)G-3' sequence.

The structure of the cationic 8,9-dihydro-8-(N7-guanyl)-9-hydroxy-aflatoxin B(1) adduct embedded in a 5'-CpG-3' sequence context and paired with deoxycytosine in the oligodeoxynucleotide d(ACATC(AFB)GATCT) x d(AGATCGATGT) was refined using molecular dynamics calculations restrained by NOE data and dihedral angle restraints obtained from NMR data. The aflatoxin moiety intercalated above the 5' face of the modified guanine. It stacked between C(5) x G(16) and (AFB)G(6) x C(15). The AFB(1) H5, OCH(3), and methylene protons faced into the minor groove, with the methylene protons oriented between the C(15) and G(16) nucleobases. The aflatoxin B(1) H6a, H8, H9, and H9a protons faced the major groove, with H6a and H9a pointing toward the 5' direction from the lesion site. The refined structure was compared to the structure of the aflatoxin B(1) adduct embedded in a 5'-ATGCAT-3' sequence in the oligodeoxynucleotide d(TAT(AFB)GCATA)(2) [Jones, W. R., Johnston, D. S., and Stone, M. P. (1998) Chem. Res. Toxicol.11, 873-881]. The structure of the intercalated aflatoxin B(1) lesion in the ATC(AFB)GAT sequence is similar to its structure in the d(AT(AFB)GCAT) sequence. This is consistent with a mechanism in which the precovalent intercalation of aflatoxin-8,9-exo-epoxide on the 5' face of guanine places the epoxide in close proximity and in the proper orientation to the N7 position of guanine, thus facilitating an S(N)2 reaction. The data provides additional insight into the nature of the disruption of the B-DNA duplex induced by aflatoxin B(1) intercalation. Overall, the results suggest that sequence contributes a minor role in modulating the structure of the cationic guanine N7 AFB(1) lesion in duplex DNA. On the other hand, structural differences are observed when the correctly paired structure is compared to the structure of the cationic AFB(1) adduct mispaired with dA [Giri, I., Johnston, D. S., and Stone, M. P. (2002) Biochemistry 41, 5462-5472].

Mispairing of the 8,9-dihydro-8-(N7-guanyl)-9-hydroxy-aflatoxin B1 adduct with deoxyadenosine results in extrusion of the mismatched dA toward the major groove.

The G --> T transversion is the dominant mutation induced by the cationic trans-8,9-dihydro-8-(N7-guanyl)-9-hydroxy-aflatoxin B(1) adduct. The structure of d(ACATC(AFB)GATCT).d(AGATAGATGT), in which the cationic adduct was mismatched with deoxyadenosine, was refined using molecular dynamics calculations restrained by NOE data and dihedral restraints obtained from NMR spectroscopy. Restrained molecular dynamics calculations refined structures with pairwise rmsd <1 A and a sixth root R1x factor between the refined structure and NOE data of 10.5 x 10-2. The mismatched duplex existed in a single conformation at neutral pH. The aflatoxin moiety intercalated above the 5' face of the modified (AFB)G. The mismatched dA was in the anti conformation about the glycosyl bond. It extruded toward the major groove and did not participate in hydrogen bonding with (AFB)G. The structure was compared with that of d(ACATCGATCT).d(AGATAGATGT) containing the corresponding unmodified G.A mismatch and with d(ACATC(AFB)GATCT).d(AGATCGATGT) containing the aflatoxin lesion in the correctly paired (AFB)G.C context. The correctly paired oligodeoxynucleotide exhibited Watson-Crick-type geometry at the (AFB)G.C pair. It melted at higher temperature than the mismatched (AFB)G.A duplex. The unmodified mismatched G.A duplex exhibited spectral line broadening at neutral pH, suggesting a mixture of conformations. It exhibited a lower melting temperature than did the mismatched (AFB)G.A duplex. These differences correlated with replication bypass experiments performed in vitro utilizing DNA polymerase I exo- [Johnston, D. S., and Stone, M. P. (2000) Chem. Res. Toxicol. 13, 1158-1164]. Those experiments showed that correct insertion of dC opposite (AFB)G blocked replication by the enzyme, whereas incorrect insertion of dA opposite (AFB)G allowed full-length replication of the adducted template strand.