Nanoscale Biodegradable Organic–Inorganic Hybrids for Efficient Cell Penetration and Drug Delivery

We report a comprehensive study on novel, highly efficient, and biodegradable hybrid molecular transporters. To this end, we designed a series of cell‐penetrating, cube‐octameric silsesquioxanes (COSS), and investigated cellular uptake by confocal microscopy and flow cytometry. A COSS with dense spatial arrangement of guanidinium groups displayed fast uptake kinetics and cell permeation at nanomolar concentrations in living HeLa cells. Efficient uptake was also observed in bacteria, yeasts, and archaea. The COSS‐based carrier was significantly more potent than cell‐penetrating peptides (CPPs) and displayed low toxicity. It efficiently delivered a covalently attached cytotoxic drug, doxorubicin, to living tumor cells. As the uptake of fluorescently labeled carrier remained in the presence of serum, the system could be considered particularly attractive for the in vivo delivery of therapeutics.     

Design and development of chemical ontologies for reaction representation

This paper describes the development of chemical ontologies applied to the representation of organic chemical reactions. The ontologies are built using the methodology known as methontology. The hierarchically structured set of terms describing the subdomains, namely, organic reactions, organic compounds, and reagents, are constructed into individual ontologies. The ontologies consist of about 200 concepts and around 125 individuals. A set of binary relations is defined in order to integrate the ontologies with applications. The ontologies are implemented as an XML application with a set of vocabulary describing the domain knowledge. This paper also features an easy-to-use chemical ontological support system (COSS) intended to represent organic chemical reactions automatically. As a model application, the automatic representation of aliphatic nucleophilic substitution reactions is demonstrated using COSS. The paper also describes a keyword-based search system whose functionality is backed with COSS.     

Nuclease tolerant FRET probe based on DNA-quantum dot conjugation.

We have developed a fluorescence resonance energy transfer (FRET) probe based on the conjugation of a quantum dot (QD) with dye (YOYO-3) intercalated DNA. The FRET-inducing electrostatic coupling of DNA and the QD made structural changes to the QD-DNA conjugates, which significantly prevented an enzymatic reaction between the DNA and a conventional restriction endonuclease (EcoRI).     

Recent Advances and Trends in Chemical CPP–Drug Conjugation Techniques

This review summarizes recent developments in conjugation techniques for the synthesis of cell-penetrating peptide (CPP)–drug conjugates targeting cancer cells. We will focus on small organic molecules as well as metal complexes that were used as cytostatic payloads. Moreover, two principle ways of coupling chemistry will be discussed direct conjugation as well as the use of bifunctional linkers. While direct conjugation of the drug to the CPP is still popular, the use of bifunctional linkers seems to gain increasing attention as it offers more advantages related to the linker chemistry. Thus, three main categories of linkers will be highlighted, forming either disulfide acid-sensitive or stimuli-sensitive bonds. All techniques will be thoroughly discussed by their pros and cons with the aim to help the reader in the choice of the optimal conjugation technique that might be used for the synthesis of a given CPP–drug conjugate     

Dielectric medium effects on collective surface plasmon coupling interactions in oligothiophene-linked gold nanoparticles

The near-field coupling interactions between surface plasmon modes of neighboring metal nanoparticles (NPs) are investigated in thin films of oligothiophene-linked Au NPs. The oligothiophene linker facilitates near-field coupling between adjacent NPs, and disruption of the conjugation in the oligothiophene by chemical oxidation leads to a decrease in surface plasmon resonance (SPR) coupling between neighboring particles. The SPR coupling between NPs was found to be highly dependent on the dielectric constant of the medium that the films are exposed to, where a higher dielectric medium leads to weaker coupling. The dependence of the SPR coupling on the dielectric constant of the medium is explained using electrodynamic theory.     

Efficient conjugation of peptides to oligonucleotides by "native ligation"

A new strategy has been developed for conjugation of peptides to oligonucleotides. The method is based on the "native ligation" of an N-terminal thioester-functionalized peptide to a 5'-cysteinyl oligonucleotide. Two new reagents were synthesized for use in solid-phase peptide and oligonucleotide synthesis, respectively. Pentafluorophenyl S-benzylthiosuccinate was used in the final coupling step in standard Fmoc-based solid-phase peptide assembly. Deprotection with trifluoracetic acid generated in solution peptides substituted with an N-terminal S-benzylthiosuccinyl moiety. O-trans-4-(N-alpha-Fmoc-S-tert-butylsulfenyl-L-cysteinyl)aminoc yclohe xyl O-2-cyanoethyl-N,N-diisopropylphosphoramidite was used in the final coupling step in standard phosphoramidite solid-phase oligonucleotide assembly. Deprotection with aqueous ammonia solution generated in solution 5'-S-tert-butylsulfenyl-L-cysteinyl functionalized oligonucleotides. Functionalized peptides and oligonucleotides were used without purification in native ligation conjugation reactions in aqueous/organic solution using tris-(2-carboxyethyl)phosphine to remove the tert-butylsulfenyl group in situ and thiophenol as a conjugation enhancer. A range of peptide-oligonucleotide conjugates were prepared by this route and purified by reversed-phase HPLC.     

Electron transfer in bis(hydrazines), a critical test for application of the Marcus model

Electron transfer in the cations of bis(hydrazines), bridged by six different π‐systems (compounds 1–6) is studied using ab initio and density functional theory (DFT) methods. Due to ionization from an antibonding combination of the lone‐pair orbitals of the nitrogens in one of the hydrazine units, conjugation is introduced in the N? N bond of that unit. This leads to a shortening of the N? N bond distance and an increase of the planarity around the nitrogens. Due to steric hindrance, this causes an increase of the angle, called φ, between the lone‐pair orbital on the nitrogen attached to the bridge and the p‐orbital on the adjacent bridge carbon for the ionized unit in the charge localized, relaxed state of the molecule. This angle controls the magnitude of the electronic coupling. In the fully delocalized symmetric transition state of the ion, however, this angle is low for both units, due to the fact that the conjugation introduced at the ionized hydrazine unit is now shared between both units. An extended π‐system is formed including the orbitals of the hydrazine units and the bridge, which leads to a large electronic coupling. The electronic coupling derived by optical methods, corresponding to the structure of the relaxed, asymmetric cation with a large φ for the ionized unit, appears to be much smaller. We believe this is due to an approximate cosine dependence on φ of the coupling. The calculations carried out support these conclusions. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 655–664, 2001     

Spectral and intramolecular charge transfer properties in terminal donor/acceptor-substituted all-trans-α,ω-diphenylpolyenes and α,ω-diphenylpolyynes

The absorption spectra and intramolecular charge transfer (CT) properties of terminal donor/acceptor-substituted all-trans-α,ω-diphenylpolyenes (DPE) and α,ω-diphenylpolyynes (DPY) molecules with different conjugated bridge length and substitution modes were investigated by using quantum chemical calculations. We calculated the ground state structures and energy of two series of terminal donor/acceptor DPE and DPY by DFT method. The dependence of conjugation length and substitution modes of the electronic absorption spectra was obtained by TDDFT calculation. The hybrid-GGA XC-functional PBE0 employed in this work was selected from several functionals by comparing the calculated electronic spectral data with experimental value. The CIS-based generalized Mulliken-Hush (GMH) approach was further used to calculate coupling values H(AD) of the CT process. The calculation shows that both the HOMO-LUMO energy gaps and average bond length alternations between unsaturated multiple (C≡C and C=C) and saturated single bonds (C-C) decrease regularly with the extension of conjugation. The effective conjugated length (ECL) of DPE and DPY with the same order MM > MP/PM > PP is found together with the regular red shift of the electronic absorption spectra with the extension of conjugation, resulting from the different π-electron delocalization and conjugation efficiency. The GMH analysis further suggests that the CT process in both DPE and DPY is predominated by the through-bond mechanism. The remarkable difference of the conjugated length dependence of squared CT coupling between substituted DPE and DPY is the result of the energetic matching degree of the frontier molecular orbitals between donor/acceptor and the conjugated bridge.     

Bioconjugation of Peptides by Palladium-Catalyzed C−C Cross-Coupling in Water

The abiotic, regioselective conjugation of peptides and proteins with non-proteinogenic structural elements requires mild and fast coupling reactions which are compatible with an aqueous reaction medium and orthogonal in their reactivity with all other functional groups in the protein. Sonogashira coupling with a palladium–guanidinophosphane catalyst that is prepared in situ (see reaction on the right) complies with these demands.     

Overcoming Symmetry Mismatch in Vaccine Nanoassembly through Spontaneous Amidation

Matching of symmetry at interfaces is a fundamental obstacle in molecular assembly. Virus‐like particles (VLPs) are important vaccine platforms against pathogenic threats, including Covid‐19. However, symmetry mismatch can prohibit vaccine nanoassembly. We established an approach for coupling VLPs to diverse antigen symmetries. SpyCatcher003 enabled efficient VLP conjugation and extreme thermal resilience. Many people had pre‐existing antibodies to SpyTag:SpyCatcher but less to the 003 variants. We coupled the computer‐designed VLP not only to monomers (SARS‐CoV‐2) but also to cyclic dimers (Newcastle disease, Lyme disease), trimers (influenza hemagglutinins), and tetramers (influenza neuraminidases). Even an antigen with dihedral symmetry could be displayed. For the global challenge of influenza, SpyTag‐mediated display of trimer and tetramer antigens strongly induced neutralizing antibodies. SpyCatcher003 conjugation enables nanodisplay of diverse symmetries towards generation of potent vaccines.     

Chemical conjugation of an mRNA cap analogue with a cell-penetrating peptide as a potential membrane permeable translation inhibitor

We present a versatile method for chemical conjugation of a dinucleotide cap analogue with a cell-penetrating peptide. The final coupling reaction is between an azide-modified peptide (MPS-N₃)—a fragment that is responsible for transport of the conjugate through the cell membrane, with a biologically active compound—and an alkynylated cap structure, using the Cu(I)-catalyzed click reaction.     

Sugar–Protein Connectivity Impacts on the Immunogenicity of Site‐Selective Salmonella O‐Antigen Glycoconjugate Vaccines

A series of glycoconjugates with defined connectivity were synthesized to investigate the impact of coupling Salmonella typhimurium O‐antigen to different amino acids of CRM₁₉₇ protein carrier. In particular, two novel methods for site‐selective glycan conjugation were developed to obtain conjugates with single attachment site on the protein, based on chemical modification of a disulfide bond and pH‐controlled transglutaminase‐catalyzed modification of lysine, respectively. Importantly, conjugation at the C186‐201 bond resulted in significantly higher anti O‐antigen bactericidal antibody titers than coupling to K37/39, and in comparable titers to conjugates bearing a larger number of saccharides. This study demonstrates that the conjugation site plays a role in determining the immunogenicity in mice and one single attachment point may be sufficient to induce high levels of bactericidal antibodies.     

Interaction-induced negative differential resistance in asymmetric molecular junctions

Combining insights from quantum chemistry calculations with master equations, we discuss a mechanism for negative differential resistance (NDR) in molecular junctions, operated in the regime of weak tunnel coupling. The NDR originates from an interplay of orbital spatial asymmetry and strong electron-electron interaction, which causes the molecule to become trapped in a nonconducting state above a voltage threshold. We show how the desired asymmetry can be selectively introduced in individual orbitals in, e.g., oligo(phenyleneethynylene)-type molecules by functionalization with a suitable side group, which is in linear conjugation to one end of the molecule and cross-conjugated to the other end.     

Bis(merocyanine) Hetero-Folda-Dimers: Evaluation of Exciton Coupling between Different Types of π-Stacked Chromphores

Exciton coupling between different types of chromophores has been rarely investigated. Herein, a systematic study on the exciton coupling between merocyanine chromophores of different conjugation length with varying excited state energies is presented. In this work well-defined hetero-dimer stacks were obtained upon folding of bis(merocyanine) dyes in nonpolar solvents. They show distinctly different absorption properties in comparison with the spectra of the single chromophores, revealing a significant coupling between the different chromophores. The simulated absorption spectra obtained from time-dependent density functional theory (TD-DFT) calculations are in good agreement with the experimental spectra. Our theoretical analysis based on an extension of Kasha's exciton theory discloses strong coupling between the dyes’ transition dipole moments despite of an excited-state energy difference of 0.60 eV between the chromophores.     

Thieno[3,4-c]pyrrole-4,6-dione-based polymer semiconductors: toward high-performance, air-stable organic thin-film transistors

We report a new p-type semiconducting polymer family based on the thieno[3,4-c]pyrrole-4,6-dione (TPD) building block, which exhibits good processability as well as good mobility and lifetime stability in thin-film transistors (TFTs). TPD homopolymer P1 was synthesized via Yamamoto coupling, whereas copolymers P2-P8 were synthesized via Stille coupling. All of these polymers were characterized by chemical analysis as well as thermal analysis, optical spectroscopy, and cyclic voltammetry. P2-P7 have lower-lying HOMOs than does P3HT by 0.24-0.57 eV, depending on the donor counits, and exhibit large oscillator strengths in the visible region with similar optical band gaps throughout the series (～1.80 eV). The electron-rich character of the dialkoxybithiophene counits in P8 greatly compresses the band gap, resulting in the lowest E(g)(opt) in the series (1.66 eV), but also raising the HOMO energy to -5.11 eV. Organic thin-film transistor (OTFT) electrical characterization indicates that device performance is very sensitive to the oligothiophene conjugation length, but also to the solubilizing side chain substituents (length, positional pattern). The corresponding thin-film microstructures and morphologies were investigated by XRD and AFM to correlate with the OTFT performance. By strategically varying the oligothiophene donor conjugation length and optimizing the solubilizing side chains, a maximum OTFT hole mobility of ～0.6 cm(2) V(-1) s(-1) is achieved for P4-based devices. OTFT environmental (storage) and operational (bias) stability in ambient was investigated, and enhanced performance is observed due to the low-lying HOMOs. These results indicate that the TPD is an excellent building block for constructing high-performance polymers for p-type transistor applications due to the excellent processability, substantial hole mobility, and good device stability.     

Synthesis and characterization of novel N-carbazole end-capped oligothiophene-fluorenes

A series of novel N-carbazole end-capped oligothiophene-fluorenes was synthesized using Ullmann coupling, bromination, and Suzuki coupling reactions. The optical, thermal, and electrochemical properties of these materials can be tuned by varying the conjugation length of the oligothiophene segment. The terminal carbazole and central fluorene moieties of the resulting materials are beneficial for their morphology, conjugation length, and solubility.     

Modified porphyrinoids from carbazates and hydrazones and the first crystal structure of a di-iminoporphodimethene

Novel porphyrinoids with interrupted conjugation (di-iminoporphodimethenes) result from the Pd-catalyzed coupling of meso-bromo porphyrins and their metal complexes with carbazates and hydrazones, followed by aerial oxidation. X-ray crystallography revealed a saddle shape for molecules of the nickel(II) complex of a di-iminoporphodimethene.     

Sulfur and Azobenzenes,a Profitable Liaison: Straightforward Synthesis of Photoswitchable Thioglycosides with Tunable Properties

Azobenzene photoswitches are valuable tools for controlling properties of molecular systems with light. We have been investigating azobenzene glycoconjugates to probe carbohydrate-protein interactions and to design glycoazobenzene macrocycles with chiroptical and physicochemical properties modulated by light irradiation. To date, direct conjugation of glycosides to azobenzenes was performed by reactions providing target compounds in limited yields. We therefore sought a more effective and reliable coupling method. In this paper, we report on a straightforward thioarylation of azobenzene derivatives with glycosyl thiols as well as other thiols, thereby increasing the scope of azobenzene conjugation. Even challenging unsymmetrical conjugates can be achieved in good yields via sequential or one-pot procedures. Importantly, red-shifted azoswitches, which are addressed with visible light, were easily functionalized. Additionally, by oxidation of the sulfide bridge to the respective sulfones, both the photochromic and the thermal relaxation properties of the core azobenzene can be tuned. Utilizing this option, we realized orthogonal three-state photoswitching in mixtures containing two distinct azobenzene thioglycosides.     

Noncrystalline phases in poly(9,9-di-n-octyl-2,7-fluorene)

Selective formation of amorphous, nematic (N), and beta phases in poly(9,9-di-n-octyl-2,7-fluorene) (PFO) films was achieved via judicious choice of process parameters. Phase structure and film morphology were carefully examined by means of X-ray diffraction as well as electron microscopy. "Amorphous" thin films were obtained by quick evaporation of solvent. Slow solvent removal during film formation or extended treatment of the amorphous film with solvent vapor resulted in predominantly the beta phase, which corresponds to a frozen (due to decreased segmental mobility upon solvent removal) and intrinsically metastable state of transformation midway between a solvent-induced clathrate phase and the equilibrium crystalline order in the undiluted state. The frozen transformation process is reactivated upon an increase in temperature beyond 100 degrees C. Compared to the amorphous film, extended backbone conjugation in the beta phase is evidenced from the emergence of a characteristic absorption peak around 430 nm near the absorption edge. For films of frozen nematic order (obtained by quenching from the nematic state), the conjugation length is also greater than the amorphous films as revealed by an absorption shoulder around 420 nm. Well-behaved single-chromophore emission with single-mode phonon coupling was observed for the beta phase; in the case of nematic films, dual-mode phonon coupling must exist if single-chromophore emission is assumed. In comparison, the emission spectrum of the amorphous film of generally shorter conjugation lengths exhibited mixed characteristics of nematic and beta phases, implying the presence of minor populations of extended conjugation similar to those in nematic and beta phases, which are of biased weightings in the emission spectra. All these films consist of nanograins (ca. 10 nm in size) of collapsed chains; the films are therefore inherently inhomogeneous in this length scale. In combination with previous observations on the crystalline (alpha and alpha') forms, the phase behavior of PFO is then generally summarized in terms of relative thermodynamic stability.