Three‐unit semicircles curve: A compact 3D graphical representation of DNA sequences based on classifications of nucleotides

A new three‐dimensional graphical representation of DNA sequences, three‐unit semicircles (TUS)‐curve, which maps a given sequence into a dot sequences embedded in three‐unit semicircles, is proposed based on three biclassifications of nucleotides. TUS‐curve has the merit of compactness and could avoid the degeneracy and loss of information. The geometrical center of the curve, which indicates the distribution of base frequencies of the corresponding DNA sequence, is extracted and applied to analyze the similarity of various species. Phylogenetic tree of 11 species based on their first exons of β‐globin genes showed that the TUS‐curve is a powerful tool to get valuable biological information. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Catalyst-free three-component approach to efficient synthesis of chromeno[4,3-b]pyrrol-4(1H)-one derivatives

A mild, efficient, and environmentally benign one-pot synthesis of functionalized chromeno[4,3-b]pyrrol-4(1H)-ones by a three-component domino reaction of 4-aminocoumarins, arylglyoxal monohydrates, and 1,3-dicarbonyl compounds in refluxing ethanol without the use of catalyst is reported. The present protocol features operational simplicity, short reaction time, good yields, and the absence of aqueous workup procedure and chromatographic separation.     

One-pot ligation strategy for atypical ubiquitin chains synthesis by using the trifluoroacetamidomethyl-protected isopeptide-linked Ub (Tfacm-isoUb) unit

Protein chemical synthesis can provide the homogeneous atypical ubiquitin chains that are usually difficult to obtain by other methods. Herein, we report a new one-pot ligation approach for the synthesis of atypical Ub chains based on the Tfacm-protected isoUb building block with operational simplicity and high efficiency. The key intermediate, the Tfacm-protected isoUb building block can be readily prepared by Fmoc SPPS. The practicality and efficiency of the new method is demonstrated by the successful preparation of K11-linked di-Ub.     

A Facile Approach to Optically Active Hydroquinoline‐2‐carboxylates by a One‐Pot Asymmetric Michael/Transamination/Cyclization Process

An efficient one‐pot synthesis of optically active hydroquinoline‐2‐carboxylates from 1,3‐cyclohexanediones, β,γ‐unsaturated α‐keto ester, and benzylamine in the presence of a chiral base catalyst and 1,8‐diazabicyclo[5.4.0]undec‐7‐ene (DBU) with good diastereoselectivity and high enantioselectivity is described. The reaction proceeds by a sequential asymmetric Michael/transamination/cyclization process.     

Photoisomerization Mechanism of Ruthenium Sulfoxide Complexes: Role of the Metal‐Centered Excited State in the Bond Rupture and Bond Construction Processes

Phototriggered intramolecular isomerization in a series of ruthenium sulfoxide complexes, [Ru(L)(tpy)(DMSO)]ⁿ⁺ (where tpy=2,2’:6’,2’’‐terpyridine; DMSO=dimethyl sulfoxide; L=2,2’‐bipyridine (bpy), n=2; N,N,N’,N’‐tetramethylethylenediamine (tmen) n=2; picolinate (pic), n=1; acetylacetonate (acac), n=1; oxalate (ox), n=0; malonate (mal), n=0), was investigated theoretically. It is observed that the metal‐centered ligand field (³MC) state plays an important role in the excited state S→O isomerization of the coordinated DMSO ligand. If the population of ³MC_S state is thermally accessible and no ³MC_O can be populated from this state, photoisomerization will be turned off because the ³MC_S excited state is expected to lead to fast radiationless decay back to the original ¹GS_S ground state or photodecomposition along the Ru²⁺?S stretching coordinate. On the contrary, if the population of ³MC_S (or ³MC_O) state is inaccessible, photoinduced S→O isomerization can proceed adiabatically on the potential energy surface of the metal‐to‐ligand charge transfer excited states (³MLCT_S→³MLCT_O). It is hoped that these results can provide valuable information for the excited state isomerization in photochromic d⁶ transition‐metal complexes, which is both experimentally and intellectually challenging as a field of study.     

Enantioselective Total Synthesis of (+)‐Steenkrotin A and Determination of Its Absolute Configuration

The first enantioselective total synthesis of (+)‐steenkrotin A has been achieved in 18 steps and 4.2 % overall yield. The key features of the strategy entail a Rh‐catalyzed O?H bond insertion followed by an intramolecular carbonyl‐ene reaction, two sequential SmI₂‐mediated Ueno–Stork and ketyl–olefin cyclizations, and a cascade intramolecular aldol condensation/vinylogous retro‐aldol/aldol process with inversion of the relative configuration at the C7 position. The absolute configuration of (+)‐steenkrotin A was determined based on the stepwise construction of the stereocenters during the total synthesis.     

Molecular dynamics simulation of DNA‐directed assembly of nanoparticle superlattices using patterned templates

DNA‐directed assembly is a well developed approach in constructing desired nano‐architectures. On the other hand, E‐beam lithography is widely utilized for high resolution nano‐scale patterning. Recently, a new technique combining these two methods was developed to epitaxially grow DNA‐mediated nanoparticle superlattices on patterned substrates. However, defects are observed in epitaxial layers which restricts this technique from building large‐scale superlattices for real applications. Here we use molecular dynamics simulations to study and predict defect formation on adsorbed superlattice monolayers. We demonstrate that this epitaxial growth is energetically driven by maximizing DNA hybridization between the epitaxial layer and the substrate and that the shape anisotropy of the DNA‐mediated template posts leads to structural defects. We also develop design rules to dramatically reduce defects on epitaxial layers. Ultimately, with the assist of the computational study, this technique will open the door to constructing well‐ordered, three‐dimensional novel nanomaterials. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 1687–1692