Enzymatic fabrication of DNA nanostructures: extension of a self-assembled oligonucleotide monolayer on gold arrays

Nucleic acid nanostructures are useful as templates for bionanofabrication of composite molecular nanostructures in materials science, molecular electronics, and biosensing. Here, we demonstrate that terminal deoxynucleotidyl transferase, which repetitively adds mononucleotides to the 3' end of a short DNA initiator, can be used to rapidly fabricate DNA nanostructures up to 121 nm high with lateral dimensions from 0.1 to 4 mum in 2 h. These programmable scaffolds can potentially be employed to build more complex nanostructures consisting of natural or unnatural nucleotides with selective docking sites along the single-stranded DNA.     

Synthesis of nonracemic allylic hydroxy phosphonates via alkene cross metathesis

Allylic hydroxy phosphonates and their derivatives can be interconverted by using cross metathesis with second generation Grubbs catalyst. The absolute stereochemistry of the starting phosphonate is conserved in the product. Cross metathesis reaction of the acrolein-derived phosphonate 2a yields a series of functionalized allylic hydroxy phosphonates. However, the cross metathesis reaction is often accompanied by competing dimerization and alkene migration reactions leading to a reduction in yield. The cinnamaldehyde- and crotonaldehyde-derived phosphonates 2b and 2c were also examined. In general, the metathesis reactions of phosphonates 2b and 2c are considerably slower than those for phosphonate 2a leading to mixtures. Several hydroxyl-protected derivatives of the phosphonate 2a (methyl carbonate 3a, acetate 4a, N-tosyl carbamate 5a, TBDMS 6a, and acetoacetate 7a) undergo metathesis without competing side reactions to give substituted allylic phosphonates in good to excellent yield.     

Synthesis,characterisation and solid state thermal behaviour of nickel(II) diamine complexes

Summary [NiL₂X₂] (L =N,N-dimethyl-1,2-ethanediamine; X = Cl^–, CF₃CO ₂ ^– , CC1₃CO ₂ ^– and CBr₃CO ₂ ^– ), [NiL₂C₂O₄] · H₂O and [NiL₂X₂] · 2 H₂O (X = Br^–, 0.5 SO ₄ ^2– and 0.5 SeO ₄ ^– ) have been synthesised and their thermal studies carried out. Thermally induced phase transition phenomena are noticed in [NiL₂X₂] (X = CF₃CO ₂ ^– and CCl₃CO ₂ ^– ) and their probable mechanisms are described. [NiL₂X₂] (X = Br^–, 0.5 SO ₄ ^2– and 0.5 SeO ₄ ^2– ) and [NiLX₂] (X = Cl^–, 0.5 C₂O ₄ ^2– and 0.5 SO ₄ ^2– ) have been prepared by solid state pyrolysis from the respective parent diamine complexes. [NiL₂X₂] have been made in solid state by temperature arrest technique from [NiL₂(CX₃CO₂)₂] (X = Cl^– and Br^–).     

Adhesion and debonding of soft elastic films: crack patterns, metastable pathways, and forces

We study the phenomenon of debonding in a thin soft elastic film sandwiched between two rigid plates as one of the plates is brought into intimate contact and then pulled away from contact proximity by application of a normal force. Nonlinear simulations based on minimization of total energy (composed of stabilizing elastic strain energy and destabilizing adhesive interaction energy) are employed to address the problems of contact hysteresis, cavitation, crack morphology, variation of contact area, snap-off distance, pull-off force, work done, and energy loss. Below a critical distance (d(c)) upon approach, simulations show the formation of columnar structures and nonrandom, regularly arranged nanocavities at the soft interface at a length scale of approximately 3h (h being the thickness of the film). The persistence of such instability upon withdrawal (distance >d(c)) indicates a contact hysteresis, which is caused by an energy barrier that separates the metastable states of the patterned configuration and the global minimum state of the flat film. The energy and the pull-off force are found to be nonequilibrium and nonunique properties depending on the initial contact, defects, noise, etc. Three broad pathways of debonding leading to adhesive failure of the interface, depending on the stiffness of the film, step size of withdrawal, and the imposed noise, are identified: a catastrophic column collapse mode, a peeling mode involving a continuous decrease in the contact area, and a column splitting mode. The first two modes are caused by a very high stress concentration near the cavity edges. These metastable patterned configurations engender pull-off forces that are orders of magnitude smaller than that required to separate two flat surfaces from contact.     

Unusually efficient quenching of the fluoroscence of an energy transfer-based optical sensor for oxygen

A two-fluorophore system consisting of pyrene as donor and perylene as energy acceptor undergoes efficient energy transfer when pyrene is electronically excited. The excitation wavelength was that of pyrene and fluorescence was monitored at the emission wavelength of perylene. The fluorescence of pyrene is strongly quenched by oxygen, but that of perylene is not. The two-fluorophore system, in contrast, is very strongly quenched, with a 4-fold increase in the Stern-Volmer quenching constant as compared to the quenching of pyrene, as a result of the effect of oxygen on the formation of the donor-acceptor exciplex, and quenching by oxygen. The results are used to design a fluorescence-based optical oxygen sensor which offers a sensitivity greatly exceeding that of existing oxygen probes.     

Kinetics and mechanism of mercury(II)-catalysed replacement of cyanide in hexacyanoferrate(II) by p-nitrosodiphenylamine

The mercury(II)-catalysed replacement of cyanide in hexacyanoferrate(II) by p-nitrosodiphenylamine (p-NDA) in aqueous solution has been investigated spectrophotometrically by measuring the change in absorbance of the green complex ion, [Fe(CN)(5).p-NDA](3-), at 640 nm. Activation parameters of the catalysed and uncatalysed reactions have been calculated. The effects of the dielectric constant and water content of the medium on reaction rates are used to explain the formation of a polar activated complex and suggest an I(d) mechanism for the catalysed reaction. The varying catalytic activity of Hg(II) as a function of concentration has been discussed.     

Beyond generative models: superfast traversal,optimization, novelty,exploration and discovery (STONED) algorithm for molecules using SELFIES

Inverse design allows the generation of molecules with desirable physical quantities using property optimization. Deep generative models have recently been applied to tackle inverse design, as they possess the ability to optimize molecular properties directly through structure modification using gradients. While the ability to carry out direct property optimizations is promising, the use of generative deep learning models to solve practical problems requires large amounts of data and is very time-consuming. In this work, we propose STONED – a simple and efficient algorithm to perform interpolation and exploration in the chemical space, comparable to deep generative models. STONED bypasses the need for large amounts of data and training times by using string modifications in the SELFIES molecular representation. First, we achieve non-trivial performance on typical benchmarks for generative models without any training. Additionally, we demonstrate applications in high-throughput virtual screening for the design of drugs, photovoltaics, and the construction of chemical paths, allowing for both property and structure-based interpolation in the chemical space. Overall, we anticipate our results to be a stepping stone for developing more sophisticated inverse design models and benchmarking tools, ultimately helping generative models achieve wider adoption.

Interpolation and exploration within the chemical space for inverse design.     

Synthesis and In Vitro Antimicrobial SAR of Benzyl and Phenyl Guanidine and Aminoguanidine Hydrazone Derivatives

A series of benzyl, phenyl guanidine, and aminoguandine hydrazone derivatives was designed and in vitro antibacterial activities against two different bacterial strains (Staphylococcus aureus and Escherichia coli) were determined. Several compounds showed potent inhibitory activity against the bacterial strains evaluated, with minimal inhibitory concentration (MIC) values in the low µg/mL range. Of all guanidine derivatives, 3-[2-chloro-3-(trifluoromethyl)]-benzyloxy derivative 9m showed the best potency with MICs of 0.5 µg/mL (S. aureus) and 1 µg/mL (E. coli), respectively. Several aminoguanidine hydrazone derivatives also showed good overall activity. Compounds 10a, 10j, and 10r–s displayed MICs of 4 µg/mL against both S. aureus and E. coli. In the aminoguanidine hydrazone series, 3-(4-trifluoromethyl)-benzyloxy derivative 10d showed the best potency against S. aureus (MIC 1 µg/mL) but was far less active against E. coli (MIC 16 µg/mL). Compound 9m and the para-substituted derivative 9v also showed promising results against two strains of methicillin-resistant Staphylococcus aureus (MRSA). These results provide new and potent structural leads for further antibiotic optimisation strategies.