A new optical strategy to determine the binding modes (intercalation vs groove binding) of small fluorescent organic molecules with calf thymus DNA was developed using two-photon absorption (TPA) spectroscopy. Two-photon excited emission was utilized to investigate a series of fluorescent nuclear dyes. The results show that TPA cross-sections are able to differentiate the fine details between the DNA binding modes. Groove binding molecules exhibit an enhanced TPA cross-section due to the DNA electric field induced enhancement of the transition dipole moment, while intercalative binding molecules exhibit a decrease in the TPA cross-section. Remarkably, the TPA cross-section of 4,6-bis(4-(4-methylpiperazin-1-yl)phenyl) pyrimidine is significantly enhanced (13.6-fold) upon binding with DNA. The sensitivity of our TPA methodology is compared to circular dichroism spectroscopy. TPA demonstrates superior sensitivity by more than an order of magnitude at low DNA concentrations. This methodology can be utilized to probe DNA interactions with other external molecules such as proteins, enzymes, and drugs.

The direct depolymerization of SiO2 to distillable alkoxysilanes has been explored repeatedly without success for 85 years as an alternative to carbothermal reduction (1900 °C) to Si(met) , followed by treatment with ROH. We report herein the base-catalyzed depolymerization of SiO2 with diols to form distillable spirocyclic alkoxysilanes and Si(OEt)4. Thus, 2-methyl-2,4-pentanediol, 2,2,4-trimethyl-1,3-pentanediol, or ethylene glycol (EGH2) react with silica sources, such as rice hull ash, in the presence of NaOH (10%) to form H2O and distillable spirocyclic alkoxysilanes [bis(2-methyl-2,4-pentanediolato) silicate, bis(2,2,4-trimethyl-1,3-pentanediolato) silicate or Si(eg)2 polymer with 5-98% conversion, as governed by surface area/crystallinity. Si(eg)2 or bis(2-methyl-2,4-pentanediolato) silicate reacted with EtOH and catalytic acid to give Si(OEt)4 in 60% yield, thus providing inexpensive routes to high-purity precipitated or fumed silica and compounds with single Si-C bonds.

The B(C 6 F 5 ) 3 catalyzed Piers-Rubinsztajn (oxysilylation) reaction of the cubic symmetry Q-cage [(HMe 2 SiOSiO 1.5 ) 8 ] with ethoxysilanes in hexane forms microporous 3-D networks coincident with ethane evolution. Slow drying provides monoliths whereas fast drying provides powders. The reaction is most efficient if initiated at 60°C for 5 min and then allowed to progress at ambient. The products offer high specific surface areas [SSAs > 700 m 2 /g, e.g. with Si(OEt) 4 ], with micropores of 0.62.0 nm, mesopores of 240 nm, total pore volumes µ 0.5 cc/g, and thermal stabilities to 320°C. Changes in reaction conditions (times, solvent volumes, catalyst concentrations) do not significantly change product properties pointing to rapid and complete reaction as evidenced by the near absence of residual SiH under all conditions for 1:1: SiH:SiOEt ratios. RSi(OEt) 3 gives similar 3-D microporous gels. Smaller R groups give higher SSAs than those with large R groups; however, R = n-octyl is not porous. Rigid, bridged compounds [(EtO) 3 SiRSi(OEt) 3 ] (R = phenyl, biphenyl) offer high SSAs whereas flexible bridges [R = (CH 2 ) 2 or 8 ] give reduced SSAs. All materials were characterized by FTIR, TGA, XRD and BET. XRD studies show periodicities suggesting some long range ordering as might be expected for reactions with cubic symmetry Q 8 cages. However, the fast reaction rates likely generate kinetic rather than thermodynamic products that cannot be expected to exhibit high degrees of ordering. Gel affinities for specific organics were studied showing some preferential ability to absorb specific solvents for example the 1:1 OHS:vinylSi(OEt) 3 gels were more selective for toluene than the 1:1 OHS:TEOS gels.

The direct depolymerization of SiO 2 to distillable alkoxysilanes has been explored repeatedly without success for 85 years as an alternative to carbothermal reduction (1900 8 8C) to Si met ,followed by treatment with ROH. We report herein the base-catalyzed depolymerization of SiO 2 with diols to form distillable spirocyclic alkoxysilanes and Si(OEt) 4 .T hus,2methyl-2,4-pentanediol, 2,2,4-trimethyl-1,3-pentanediol, or ethylene glycol (EGH 2 )r eact with silica sources,s uch as rice hull ash, in the presence of NaOH (10 %) to form H 2 Oa nd distillable spirocyclic alkoxysilanes [bis(2-methyl-2,4-pentanediolato) silicate,bis(2,2,4-trimethyl-1,3-pentanediolato) silicate or Si(eg) 2 polymer with 5-98 %c onversion, as governed by surface area/crystallinity.S i(eg) 2 or bis(2-methyl-2,4-pentanediolato) silicate reacted with EtOH and catalytic acid to give Si(OEt) 4 in 60 %y ield, thus providing inexpensive routes to high-purity precipitated or fumed silica and compounds with single SiÀCb onds.

The classical model for DNA groove binding states that groove binding molecules should adopt a crescent shape that closely matches the helical groove of DNA. Here, we present a new design strategy that does not obey this classical model. The DNA-binding mechanism of small organic molecules was investigated by synthesizing and examining a series of novel compounds that bind with DNA. This study has led to the emergence of structure-property relationships for DNA-binding molecules and/or drugs, which reveals that the structure can be designed to either intercalate or groove bind with calf thymus dsDNA by modifying the electron acceptor properties of the central heterocyclic core. This suggests that the electron accepting abilities of the central core play a key role in the DNA-binding mechanism. These small molecules were characterized by steady-state and ultrafast nonlinear spectroscopies. Bioimaging experiments were performed in live cells to evaluate cellular uptake and localization of the novel small molecules. This report paves a new route for the design and development of small organic molecules, such as therapeutics, targeted at DNA as their performance and specificity is dependent on the DNA-binding mechanism.