Imidazolo‐dC Metal‐Mediated Base Pairs: Purine Nucleosides Capture Two Ag+ Ions and Form a Duplex with the Stability of a Covalent DNA Cross‐Link

8‐Phenylimidazolo‐dC (^phImidC, 2 ) forms metal‐mediated DNA base pairs by entrapping two silver ions. To this end, the fluorescent “purine” 2′‐deoxyribonucleoside 2 has been synthesised and converted into the phosphoramidite 6 . Owing to the ease of nucleobase deprotonation, the new Ag⁺‐mediated base pair containing a “purine” skeleton is much stronger than that derived from the pyrrolo‐ [3,4‐d]pyrimidine system (^phPyrdC, 1 ). The silver‐mediated ^phImidC–^phImidC base pair fits well into the DNA double helix and has the stability of a covalent cross‐link. The formation of such artificial metal base pairs might not be limited to DNA but may be applicable to other nucleic acids such as RNA, PNA and GNA as well as other biopolymers.     

Uncovering the Intramolecular Emission and Tuning the Nonlinear Optical Properties of Organic Materials by Cocrystallization

The spectroscopic and photophysical properties of organic materials in the solid‐state are widely accepted as a result of their molecular packing structure and intermolecular interactions, such as J‐ and H‐aggregation, charge‐transfer (CT), excimer and exciplex. However, in this work, we show that Spe‐F₄DIB cocrystals (SFCs) surprisingly retain the energy levels of photoluminescence (PL) states of Spe crystals, despite a significantly altered molecular packing structure after cocrystallization. In comparison, Npe‐F₄DIB cocrystals (NFCs) with new spectroscopic states display different spectra and photophysical behaviors as compared with those of individual component crystals. These may be related to the molecular configuration in crystals, and we propose Spe as an “intramolecular emissive” material, thus providing a new viewpoint on light‐emitting species of organic chromophores. Moreover, the nonlinear optical (NLO) properties of Npe and Spe are firstly demonstrated and modulated by cocrystallization. The established “molecule‐packing‐property” relationship helps to rationally control the optical properties of organic materials through cocrystallization.     

Possible incorporation of the purine–purine mispairs in the DNA helix and the interpretation of the transversion-type point mutations

The stereochemical and energetic compatibility of incorporation of the non-Watson–Crick hydrogen bonded purine–purine base pairs of normal tautomers in the helical structure of B-DNA is studied here. The hydrogen bonding positions of the possible “mispairs” of the bases GA, GG, and AA are optimized first in the base plane by translational and rotational movement along the hydrogen bonds and then introduced at an appropriate position in the DNA structure. The optimum backbone geometries which can accommodate the “mispairs” are obtained by force field computations. The stereochemical and energetic aspects of the various mispairs are discussed in light of their possible incorporation in DNA and as mutational intermediates for the “transversion”-type point mutations.     

A concept for bifocal contact‐ or intraocular lenses: liquid single crystal hydrogels (“LSCH”)

The synthesis of liquid single crystal hydrogels (“LSCH”) in suitable molds offers an innovative concept to realize bifocal contact‐ or intraocular‐lenses. LSCH combine the properties required for applications as bifocal ophthalmic lenses: the soft and water‐containing hydrogel enables oxygen permeation and exhibits high birefringence due to the liquid crystalline phase structure built up by rigid rod‐like amphiphiles. Via a photo‐initiated crosslinking reaction of aqueous solutions of monomeric lyotropic liquid crystalline amphiphiles in the macroscopically ordered liquid crystalline state, we obtain optically uniaxially ordered and transparent LSCH. The orientation process and the phase structure of the anisotropic hydrogel is analyzed by deuterium NMR‐spectroscopy. Copyright © 2002 John Wiley & Sons, Ltd.     

Dielectrophoretic trapping of multilayer DNA origami nanostructures and DNA origami‐induced local destruction of silicon dioxide

DNA origami is a widely used method for fabrication of custom‐shaped nanostructures. However, to utilize such structures, one needs to controllably position them on nanoscale. Here we demonstrate how different types of 3D scaffolded multilayer origamis can be accurately anchored to lithographically fabricated nanoelectrodes on a silicon dioxide substrate by DEP. Straight brick‐like origami structures, constructed both in square (SQL) and honeycomb lattices, as well as curved “C”‐shaped and angular “L”‐shaped origamis were trapped with nanoscale precision and single‐structure accuracy. We show that the positioning and immobilization of all these structures can be realized with or without thiol‐linkers. In general, structural deformations of the origami during the DEP trapping are highly dependent on the shape and the construction of the structure. The SQL brick turned out to be the most robust structure under the high DEP forces, and accordingly, its single‐structure trapping yield was also highest. In addition, the electrical conductivity of single immobilized plain brick‐like structures was characterized. The electrical measurements revealed that the conductivity is negligible (insulating behavior). However, we observed that the trapping process of the SQL brick equipped with thiol‐linkers tended to induce an etched “nanocanyon” in the silicon dioxide substrate. The nanocanyon was formed exactly between the electrodes, that is, at the location of the DEP‐trapped origami. The results show that the demonstrated DEP‐trapping technique can be readily exploited in assembling and arranging complex multilayered origami geometries. In addition, DNA origamis could be utilized in DEP‐assisted deformation of the substrates onto which they are attached.     

Crystal structure of a NIR‐Emitting DNA‐Stabilized Ag16 Nanocluster

DNA has been used as a scaffold to stabilize small, atomically monodisperse silver nanoclusters, which have attracted attention due to their intriguing photophysical properties. Herein, we describe the X‐ray crystal structure of a DNA‐encapsulated, near‐infrared emitting Ag₁₆ nanocluster (DNA–Ag₁₆NC). The asymmetric unit of the crystal contains two DNA–Ag₁₆NCs and the crystal packing between the DNA–Ag₁₆NCs is promoted by several interactions, such as two silver‐mediated base pairs between 3′‐terminal adenines, two phosphate–Ca²⁺–phosphate interactions, and π‐stacking between two neighboring thymines. Each Ag₁₆NC is confined by two DNA decamers that take on a horse‐shoe‐like conformation and is almost fully shielded from the solvent environment. This structural insight will aid in the determination of the structure/photophysical property relationship for this class of emitters and opens up new research opportunities in fluorescence imaging and sensing using noble‐metal clusters.     

A Family of “Click” Nucleosides for Metal‐Mediated Base Pairing: Unravelling the Principles of Highly Stabilizing Metal‐Mediated Base Pairs

A family of artificial nucleosides has been developed by applying the Cu^I‐catalyzed Huisgen 1,3‐dipolar cycloaddition. Starting from 2‐deoxy‐β‐D ‐glycosyl azide as a common precursor, three bidentate nucleosides have been synthesized. The 1,2,3‐triazole involved in all three nucleobases is complemented by 1,2,4‐triazole ( TriTri ), pyrazole ( TriPyr ), or pyridine ( TriPy ). Molecular structures of two metal complexes indicate that metal‐mediated base pairs of TriPyr may not be fully planar. An investigation of DNA oligonucleotide duplexes comprising the new “click” nucleosides showed that they can bind Ag^I to form metal‐mediated base pairs. In particular the mispair formed from TriPy and the previously established imidazole nucleoside is significantly stabilized in the presence of Ag^I. A comparison of different oligonucleotide sequences allowed the determination of general factors involved in the stabilization of nucleic acids duplexes with metal‐mediated base pairs.     

Frustrated Lewis Pairs: Metal‐free Hydrogen Activation and More

Sterically encumbered Lewis acid and Lewis base combinations do not undergo the ubiquitous neutralization reaction to form “classical” Lewis acid/Lewis base adducts. Rather, both the unquenched Lewis acidity and basicity of such sterically “frustrated Lewis pairs (FLPs)” is available to carry out unusual reactions. Typical examples of frustrated Lewis pairs are inter‐ or intramolecular combinations of bulky phosphines or amines with strongly electrophilic RB(C₆F₅)₂ components. Many examples of such frustrated Lewis pairs are able to cleave dihydrogen heterolytically. The resulting H⁺/H^? pairs (stabilized for example, in the form of the respective phosphonium cation/hydridoborate anion salts) serve as active metal‐free catalysts for the hydrogenation of, for example, bulky imines, enamines, or enol ethers. Frustrated Lewis pairs also react with alkenes, aldehydes, and a variety of other small molecules, including carbon dioxide, in cooperative three‐component reactions, offering new strategies for synthetic chemistry.     

Self‐Assembly of Pyridinium‐Functionalized Anthracenes: Molecular‐Skeleton‐Directed Formation of Microsheets and Microtubes

Two amphiphilic regioisomers, 9‐AP (1‐[11‐(9‐anthracenylmethoxy)‐11‐oxoundecyl]pyridinium bromide), and 2‐AP (1‐[11‐(2‐anthracenyl methoxy)‐11‐oxoundecyl]pyridinium bromide), were synthesized and their assembly behaviors were studied. Due to the anisotropic features of the anthracene structure, different substituted positions on the anthracene ring lead 9‐AP and 2‐AP to adapt “shaver” and “spatula”‐like molecular shapes, respectively, which consequently dictate the structure of their final assemblies. While “shaver”‐shaped 9‐AP assembled into microsheets, driven by π–π interactions, “spatula”‐shaped 2‐AP assembled into microtubular structures, promoted primarily by charge‐transfer interactions.     

A cationic dye triplet as a unique "glue" that can connect fully matched termini of DNA duplexes

In this study, we propose that three consecutive cationic p‐methylstilbazoles tethered on D ‐threoninols ( Z residues) at 5′ termini act as a unique “glue” connecting DNA duplexes by their interstrand cluster formation. Interstrand clustering of p‐methylstilbazoles ( ZZZ triplets) induces narrowing and hypsochromic shift of bands at 350 nm, which can be assigned to the absorption of p‐methylstilbazole. However, single‐stranded DNA conjugates involving a ZZZ triplet at the 5′ terminus of 8‐mer native nucleotides is found not to induce such large spectral changes, which implies that the intrinsic self‐assembling property of ZZZ triplets is weak. Interestingly, when this conjugate is hybridized with a complementary 8‐mer native oligonucleotide, a remarkable spectral change is observed, indicating the dimerization of a duplex through the interstrand clustering of ZZZ triplets. Dimerization of the duplex is also evidenced by cold‐spray ionization mass spectrometry. This interstrand clustering is observed only when a ZZZ triplet is tethered to a 5′ rather than 3′ terminus. Furthermore, the stability of the interstrand cluster increases by increasing the number of nucleobases of the DNA portion, and when mismatched base pairs are incorporated or when a base next to the Z residue is deleted, the stability substantially drops. When we apply the ZZZ triplet to the formation of a nanowire using two complementary DNA conjugates, each of which has a ZZZ triplet at the 5′ termini as overhang, we demonstrate the successful formation of a nanowire by native PAGE analysis. Since native sticky ends that have three nucleotides do not serve as “glue”, ZZZ triplets with their unique glue‐like properties are prime candidates for constructing DNA‐based nanoarchitectures.     

Synthesis and aggregation behavior of chitooligosaccharide‐based biodegradable graft copolymers

A series of novel “jellyfish‐like” graft copolymers with chitooligosaccharide (COS) as shorter backbone and poly(ε‐caprolactone) as longer branches were synthesized using ring‐opening polymerization of ε‐caprolactone via a protection‐polymerization‐deprotection procedure with trimethylsilylchitooligosaccharide as intermediate and triethylaluminum as catalyst precursor. The obtained chitooligosaccharide‐graft‐poly(ε‐caprolactone) polymers possess amphiphilic structure with hydrophilic COS backbone and hydrophobic polycaprolactone branches. Because of this unique “jellyfish‐like” structure, these graft copolymers could self‐assemble to form various morphologies of aggregates in a mixture solution of water and tetrahydrofuran. The transmission electron microscopy studies revealed that the formed aggregates exhibited necklace‐like, flower‐like onion vesicle, and tubular morphologies. It is found that the hydrogen‐bonding formed by the hydroxyl and amino groups remained on the COS backbone played an important role during the aggregation of these graft copolymers, and their morphologies were changed with the varying length of poly (ε‐caprolactone) branches, the concentration of the graft copolymer, and the self‐assembly process. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4889–4904, 2008     

Reconstruction of Protein‐Like Globular Structure for Random and Designed Copolymers

We present the results of computer simulation of Langevin dynamics of AB‐copolymer coil‐globule transition. The method for estimation of the quality of reconstruction of protein‐like globular structure after cooling procedure is proposed. We study specially designed “protein‐like” and random primary sequences and carry out a comparative analysis of the corresponding globular conformations for different intramolecular interactions. It is found that the energy of intramolecular interactions, as well as the type of primary sequence, are important in the process of parent globular structure reconstruction. As a rule, protein‐like sequences exhibit better reconstruction of initial globular structure after cooling procedure. There is a region of energy parameters enabling optimum reconstruction of initial globular structure.     

Crystal Structures of Dimethoxyanthracens: A Clue to a Rational Design of Packing Structures of π‐Conjugated Molecules

We carried out a systematic investigation of packing structures of a series of dimethoxyanthracenes, i. e., 1,4‐ ( 1 ), 1,8‐ ( 2 ), 1,5‐ ( 3 ), 2,6‐ ( 4 ), and 2,7‐derivatives ( 5 ). The packing structures of the dimethoxyanthracenes are classified into two types, a rubrene‐like pitched π‐stack ( 1 – 3 ) and a typical herringbone packing ( 4 and 5 ), which evidently show that the position of methoxy groups is crucial to determine the packing structure of dimethoxyanthracenes. Effects of the substitution position on intermolecular interactions are analyzed by the noncovalent intermolecular interaction (NCI) method, Hirshfeld surface analysis, and symmetry‐adapted perturbation theory (SAPT) method, thus clarifying active roles of the methoxy groups in the formation of rubrene‐like pitched π‐stack. The present results shed light on a molecular design strategy to realize the rubrene‐like pitched π‐stack in the solid state, which had been regarded as a packing structure limited for rubrene and its closely related derivatives.     

A new strategy for synthesis of “umbrella‐like” poly(ethylene glycol) with monofunctional end group for bioconjugation

A novel strategy was used to synthesize poly(ethylene glycol) (PEG) with “umbrella‐like” structure containing a single reactive group at the “handle” of the “umbrella”. 1‐(Bis(2‐hydroxyethyl)amino)‐3‐(1‐ethoxyethoxy)propan‐2‐ol was used to initiate the ring‐opening polymerization (ROP) of ethylene oxide (EO) in the presence of diphenylmethylpotassium (DPMK) to obtain three‐arm PEG (PEG3), then terminated by benzyl bromide or ethyl bromide. The resultant PEG3 was hydrolyzed to generate hydroxyl group at the conjunction point, and the second step ROP of EO was carried out using PEG3‐OH as macroinitiator in the presence of DPMK. The obtained four‐arm PEG (PEG4) contained a functional hydroxyl group at the end of the fourth arm, which could be easily modified to bioactive groups such as carboxyl, active ester, amino, etc. The well‐defined structure of “umbrella‐like” PEG was characterized by GPC, ¹H NMR, and MALDI‐TOF MS in detail. Propionic acid succinimidyl ester of PEG4 (10 kDa) was utilized for protein conjugation with interferon α‐2b. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010     

Spectroscopic,Thermal and Structural Studies of Aza‐aromatic Base Adducts of Cadmium Furoyltrifluoroacetonate

Three aza‐aromatic base adducts of cadmium(II) furoyltrifluoroacetonate, [Cd(4,4′‐bpy)(ftfa)₂]_n ( 1 ), [Cd(2,2′‐bpy)(ftfa)₂] ( 2 ) and [Cd(dmp)(ftfa)₂] ( 3 ) (“4,4′‐bpy”, “2,2′‐bpy”, “dmp” and “ftfa” are the abbreviations of 4,4′‐bipyridine, 2,2′‐bipyridine, 2,9‐dimethyl‐1,10‐phenanthroline and furoyltrifluoroacetonate, respectively) have been synthesized and characterized by elemental analysis and IR, ¹H NMR and ¹³C NMR spectroscopy and studied by thermal as well as X‐ray crystallography. The single‐crystal structure of these complexes shows that the coordination number of the Cd^II ions are six with two N‐donor atoms from aza‐aromatic base ligands and four O‐donors from two the furoyltrifluoroacetonates. The supramolecular features in these complexes are guided/controlled by weak directional intermolecular interactions.     

Thread Insertion of a Bis(dipyridophenazine) Diruthenium Complex into the DNA Double Helix by the Extrusion of AT Base Pairs and Cross‐Linking of DNA Duplexes

The crystal structure of the Δ,Δ enantiomer of the binuclear “light‐switch” ruthenium complex [μ‐(11,11′‐bidppz)(1,10‐phenanthroline)₄ Ru₂]⁴⁺ bound to the oligonucleotide d(CGTACG) shows that one dppz moiety of the dumbbell‐like compound inserts into the DNA stack through the extrusion of an AT base pair. The second dppz moiety recruits a neighboring DNA molecule, and the complex thus cross‐links two adjacent duplexes by bridging their major grooves.     

Unconventional consideration of the symmetry properties—New techniques and computer codes: Application for high‐temperature superconductors

The conventional technique for solving the equations of quantum chemistry is extended to the structures possessing certain symmetries. This proposal allows the release of unoccupied electronic states located lower than the ground‐state Fermi level of a specific system. Such states can be treated as “spectral holes.” Application of this technique, in particular, when calculating the electronic structure of the high‐temperature superconductor (HTSC) compound YBa₂Cu₃O_{7? δ} (0 ≤ δ ≤ 1) results in the following. For all versions of the examined charge distributions over a crystal lattice, spectral holes of high spatial localization are found. The “spatial spectral holes” are located mainly at the p_y‐orbitals of the apex oxygens. These orbitals overlap and form linear chains that are parallel to the known Cu(1)? O chains, disappearing when δ is close to 1. One can suppose that the linear chains of the overlapping hole states form a “superconducting channel.” Some other parameters closely related to the critical characteristics of HTSC materials are also calculated. The calculations show that the superconducting channel is broken when the oxygen chain atoms O(1) are removed (δ > 0). © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Nanocatalosomes as Plasmonic Bilayer Shells with Interlayer Catalytic Nanospaces for Solar‐Light‐Induced Reactions

Interest and challenges remain in designing and synthesizing catalysts with nature‐like complexity at few‐nm scale to harness unprecedented functionalities by using sustainable solar light. We introduce “nanocatalosomes”—a bio‐inspired bilayer‐vesicular design of nanoreactor with metallic bilayer shell‐in‐shell structure, having numerous controllable confined cavities within few‐nm interlayer space, customizable with different noble metals. The intershell‐confined plasmonically coupled hot‐nanospaces within the few‐nm cavities play a pivotal role in harnessing catalytic effects for various organic transformations, as demonstrated by “acceptorless dehydrogenation”, “Suzuki–Miyaura cross‐coupling” and “alkynyl annulation” affording clean conversions and turnover frequencies (TOFs) at least one order of magnitude higher than state‐of‐the‐art Au‐nanorod‐based plasmonic catalysts. This work paves the way towards next‐generation nanoreactors for chemical transformations with solar energy.     

Solution Structure,Mechanism of Replication,and Optimization of an Unnatural Base Pair

As part of an ongoing effort to expand the genetic alphabet for in vitro and eventual in vivo applications, we have synthesized a wide variety of predominantly hydrophobic unnatural base pairs and evaluated their replication in DNA. Collectively, the results have led us to propose that these base pairs, which lack stabilizing edge‐on interactions, are replicated by means of a unique intercalative mechanism. Here, we report the synthesis and characterization of three novel derivatives of the nucleotide analogue d MMO2 , which forms an unnatural base pair with the nucleotide analogue d 5SICS . Replacing the para‐methyl substituent of d MMO2 with an annulated furan ring (yielding d FMO ) has a dramatically negative effect on replication, while replacing it with a methoxy (d DMO ) or with a thiomethyl group (d TMO ) improves replication in both steady‐state assays and during PCR amplification. Thus, d TMO –d 5SICS , and especially d DMO –d 5SICS , represent significant progress toward the expansion of the genetic alphabet. To elucidate the structure–activity relationships governing unnatural base pair replication, we determined the solution structure of duplex DNA containing the parental d MMO2 –d 5SICS pair, and also used this structure to generate models of the derivative base pairs. The results strongly support the intercalative mechanism of replication, reveal a surprisingly high level of specificity that may be achieved by optimizing packing interactions, and should prove invaluable for the further optimization of the unnatural base pair.