Synthesis and characterization of a novel crystalline AlPO4 molecular sieve,CFAP-7

The novel crystalline aluminophosphate CFAP-7, having a characteristic X-ray powder diffraction pattern, has been synthesized hydrothermally in a system consisting of di-n-butylamine-(NH₄)₂O–P₂O₅–Al₂O₃–H₂O at 120 to 140°C, the P₂O₅ and Al₂O₃ sources of which were provided by (NH₄)₃PO₄·3H₂O and Al₂(SO₄)₃ in aqueous solution, respectively. Investigations by DTA, TG, DTG, XRD, and IR indicate transformation of the original product (form A) into more stable crystal forms B and C on heating at about 180°C and 240°C, respectively, while liberating water and amine. Isotherms for the adsorption of water and methanol at 23°C show that both form B and form C are molecular sieves with a window dimension of 4.3–4.9 Å, and a methanol volume adsorbtion greater than that of water.     

Topological study of a hypothetical molecular sieve MCR-16 with extra-large open pores

The topology of the framework of a novel zeolite, named MCR-16, with cylindrical channels spanned by the 16-membered ring, is constructed, in which the sigma transformation is a conceptual device for inter-relating the known zeolite mordenite and the hypothetical MCR-16. The consistent molecular mechanics force field is used as the foundation for the discussion on the steric energy of the structure. The configuration energy is minimized by the simulated annealing method. The consequent Si–O, Si–Si and O–O distances and Si–O–Si and O–Si–O angles of the designed MCR-16 structure are all within the limits of the reasonable ranges.     

Synthesis of a new zeolite structure ITQ-24, with intersecting 10- and 12-membered ring pores

A new 10- and 12-membered ring zeolite, named ITQ-24, has been synthesized, and its structure has been solved. It has been found that this zeolite structure is topologically identical to that proposed for the hypothetical polymorph C of the SSZ-33/SSZ-26/CIT-1 family. This new zeolite has been achieved by using a rational approach of introducing Ge in the framework that has a directing effect toward zeolite structures with double-four-membered rings as secondary building units. Notoriously, active catalytic centers, such as Ti and Al, have been incorporated into this new zeolite, demonstrating that it is catalytically active for alkylation of aromatics.     

Speeding up biomolecular interactions by molecular sledding

Numerous biological processes involve association of a protein with its binding partner, an event that is preceded by a diffusion-mediated search bringing the two partners together. Often hindered by crowding in biologically relevant environments, three-dimensional diffusion can be slow and result in long bimolecular association times. Similarly, the initial association step between two binding partners often represents a rate-limiting step in biotechnologically relevant reactions. We demonstrate the practical use of an 11-a.a. DNA-interacting peptide derived from adenovirus to reduce the dimensionality of diffusional search processes and speed up associations between biological macromolecules. We functionalize binding partners with the peptide and demonstrate that the ability of the peptide to one-dimensionally diffuse along DNA results in a 20-fold reduction in reaction time. We also show that modifying PCR primers with the peptide sled enables significant acceleration of standard PCR reactions.     

Accurate molecular weight determination of small molecules via DOSY-NMR by using external calibration curves with normalized diffusion coefficients

Determination of the aggregation and solvation numbers of organometallic complexes in solution is an important task to increase insight in reaction mechanisms. Thus knowing which aggregates are formed during a reaction is of high interest to develop better selectivity and higher yields. Diffusion-ordered spectroscopy (DOSY), which separates NMR signals according to the diffusion coefficient, finds increasing use to identify species in solution. However, there still is no simple relationship between diffusion coefficient and molecular weight (MW). Some methods have been developed to estimate the MW but still with a significant error of ±30%. Here we describe a novel development of MW-determination by using an external calibration curve (ECC) approach with normalized diffusion coefficients. Taking the shape of the molecules into account enables accurate MW-predictions with a maximum error of smaller than ±9%. Moreover we show that the addition of multiple internal references is dispensable. One internal reference (that also can be the solvent) is sufficient. If the solvent signal is not accessible, 16 other internal standards (aliphatics and aromatics) are available to avoid signal overlapping problems and provide flexible choice of analytes. This method is independent of NMR-device properties and diversities in temperature or viscosity and offers an easy and robust method to determine accurate MWs in solution.     

Synthesis of triazolium-based mono- and tris-branched [1]rotaxanes using a molecular transporter of dibenzo-24-crown-8

We report a diverted route to [1]rotaxane and tris-branched [1]rotaxane that are devoid of any efficient template and which could not be obtained by classical straightforward strategies. The described chemical route relies on the utilization of a “macrocycle transporter”, which is able first to bind a macrocycle, second to link temporarily a triazolium-containing molecular axle, and third to deliver the macrocycle around the new docked axle through molecular machinery in a [1]rotaxane structure. The extended encircled thread is eventually cleaved by an amine or a triamine to afford the triazolium-containing [1]rotaxanes, releasing at the same time, the macrocycle transporter as a recyclable species.     

A crystalline sponge based on dispersive forces suitable for X-ray structure determination of included molecular guests

A crystalline porous material showing one-dimensional (1-D) rectangular micropores (12 × 9 Ų) has been assembled from a semirigid macrocyclic tetraimine and EtOAc as the templating agent. The 1-D nature of the material is intrinsic to the conformationally rigid structure of a macrocyclic sub-unit bearing four cyclohexylidene residues. The multiple dispersive forces established among the aliphatic residues glutted the 1-D channels and provided thermal stability to the material at temperatures below 160 °C. Upon removal of the template, the structure of the empty solid exhibited permanent microporosity (S _BET = 342 m² g^–1). Being a true molecular sponge, the channel framework of this material allowed the inclusion of a variety of molecular sample guests without compromising its crystalline nature. Remarkably, this crystalline material enabled the structure determination by X-ray diffraction of the included molecules. Theoretical studies demonstrated the vital role played by the dispersive forces in the overall stabilization of the crystal packing.     

Experiences with a researcher-centric ELN

Electronic Laboratory Notebooks (ELNs) are progressively replacing traditional paper books in both commercial research establishments and academic institutions. University researchers require specific features from ELNs, given the need to promote cross-institutional collaborative working, to enable the sharing of procedures and results, and to facilitate publication. The LabTrove ELN, which we use as our exemplar, was designed to be researcher-centric (i.e., not only aimed at the individual researcher''s basic needs rather than to a specific institutional or subject or disciplinary agenda, but also able to be tailored because it is open source). LabTrove is being used in a heterogeneous set of academic laboratories, for a range of purposes, including analytical chemistry, X-ray studies, drug discovery and a biomaterials project. Researchers use the ELN for recording experiments, preserving data collected, and for project coordination. This perspective article describes the experiences of those researchers from several viewpoints, demonstrating how a web-based open source electronic notebook can meet the diverse needs of academic researchers.     

A new aluminosilicate molecular sieve with a system of pores between those of ZSM-5 and beta zeolite

A new aluminosilicate zeolite (ITQ-39) has been synthesized. This is an extensively faulted structure with very small domains that makes the structure elucidation very difficult. However, a combination of adsorption spectroscopy and reactivity studies with selected probe molecules suggests that the pore structure of ITQ-39 is related to that of Beta zeolite, with a three-directional channel system with large pores (12-MR), but with an effective pore diameter between those of Beta and ZSM-5, or a three-directional channel system with interconnected large (12-MR) and medium pores (10-MR). The pore topology of ITQ-39 is very attractive for catalysis and shows excellent results for the preparation of cumene by alkylation of benzene, while it can be a promising additive for FCC.     

Crystal and molecular structure of novel 10-membered ring compound: 10-Chloro-1,7-ditosyl-8-phenyl-4,1,7-benzoxadiazecine

10-Chloro-1,7-ditosyl-8-phenyl-4,1,7-benzoxadiazecine is obtained by reacting the sodium salt of N , N ′-ditosyl-2-amino-5-chlorobenzhydrylamine with the ditosylate of bis(hydroxyethyl) ether in DMF. The structure of the title compound was established by X-ray crystal structure analysis. The 10-membered ring that is the core of the molecule is asymmetric and considerably folded. © 1995 John Wiley & Sons, Inc.     

Image-guided combination chemotherapy and photodynamic therapy using a mitochondria-targeted molecular probe with aggregation-induced emission characteristics

Subcellular targeted cancer therapy and in situ monitoring of therapeutic effect are highly desirable for clinical applications. Herein, we report a series of probes by conjugating zero (TPECM-2Br), one (TPECM-1TPP) and two (TPECM-2TPP) triphenylphosphine (TPP) ligands to a fluorogen with aggregation-induced emission (AIE) characteristics. The probes are almost non-emissive as molecularly dissolved species, but they can light up in cell cytoplasm or mitochondria. TPECM-2TPP is found to be able to target mitochondria, depolarize mitochondria membrane potential and selectively exert potent chemo-cytotoxicity on cancer cells. Furthermore, it can efficiently generate singlet oxygen with strong photo-toxicity upon light illumination, which further enhances its anti-cancer effect. On the other hand, TPECM-1TPP can also target mitochondria and generate singlet oxygen to trigger cancer cell apoptosis, but it shows low cytotoxicity in dark. Meanwhile, TPECM-1TPP can report the cellular oxidative stress by visualizing the morphological changes of mitochondria. However, TPECM-2Br does not target mitochondria and shows no obvious anticancer effect either in dark or under light illumination. This study thus highlights the importance of molecular probe design, which yields a new generation of subcellular targeted molecular theranostic agents with multi-function, such as cancer cell imaging, chemotherapy, photodynamic therapy, and in situ monitoring of the therapeutic effect in one go.     

Absolute structure determination of compounds with axial and planar chirality using the crystalline sponge method

The absolute stereochemistry of compounds with axial and planar chirality is successfully determined by the crystalline sponge method without crystallization or derivatization of the compounds. This method is applied to absolute structure determination in the asymmetric synthesis of unique compounds with axial and planar chirality.     

Reaction of a diaryldigermyne with ethylene

Reaction of the stable digermyne BbtGeGeBbt (Bbt = 2,6-[CH(SiMe₃)₂]₂-4-[C(SiMe₃)₃]-C₆H₂) with ethylene initially afforded the corresponding 1,2-digermacyclobutene. Depending on the reaction conditions applied, further reaction of this 1,2-digermacyclobutene with ethylene furnished two different reaction products: a 1,4-digermabicyclo[2.2.0]hexane or a bis(germiranyl)ethane. Combined experimental and theoretical results suggested that the 1,4-digermabicyclo[2.2.0]hexane and the bis(germiranyl)ethane are the thermodynamic and kinetic reaction products, respectively. A reaction mechanism in agreement with these results was proposed.     

Unravelling the pH-dependence of a molecular photocatalytic system for hydrogen production

Photocatalytic systems for the reduction of aqueous protons are strongly pH-dependent, but the origin of this dependency is still not fully understood. We have studied the effect of different degrees of acidity on the electron transfer dynamics and catalysis taking place in a homogeneous photocatalytic system composed of a phosphonated ruthenium tris(bipyridine) dye (RuP) and a nickel bis(diphosphine) electrocatalyst (NiP) in an aqueous ascorbic acid solution. Our approach is based on transient absorption spectroscopy studies of the efficiency of photo-reduction of RuP and NiP correlated with pH-dependent photocatalytic H₂ production and the degree of catalyst protonation. The influence of these factors results in an observed optimum photoactivity at pH 4.5 for the RuP–NiP system. The electron transfer from photo-reduced RuP to NiP is efficient and independent of the pH value of the medium. At pH <4.5, the efficiency of the system is limited by the yield of RuP photo-reduction by the sacrificial electron donor, ascorbic acid. At pH >4.5, the efficiency of the system is limited by the poor protonation of NiP, which inhibits its ability to reduce protons to hydrogen. We have therefore developed a rational strategy utilising transient absorption spectroscopy combined with bulk pH titration, electrocatalytic and photocatalytic experiments to disentangle the complex pH-dependent activity of the homogenous RuP–NiP photocatalytic system, which can be widely applied to other photocatalytic systems.     

Molecular glues for manipulating enzymes: trypsin inhibition by benzamidine-conjugated molecular glues

Water-soluble bioadhesive polymers bearing multiple guanidinium ion (Gu⁺) pendants at their side-chain termini (Glue_n–BA, n = 10 and 29) that were conjugated with benzamidine (BA) as a trypsin inhibitor were developed. The Glue_n–BA molecules are supposed to adhere to oxyanionic regions of the trypsin surface, even in buffer, via a multivalent Gu⁺/oxyanion salt-bridge interaction, such that their BA group properly blocks the substrate-binding site. In fact, Glue₁₀–BA and Glue₂₉–BA exhibited 35- and 200-fold higher affinities for trypsin, respectively, than a BA derivative without the glue moiety (TEG–BA). Most importantly, Glue₁₀–BA inhibited the protease activity of trypsin 13-fold more than TEG–BA. In sharp contrast, ^mGlue₂₇–BA, which bears 27 Gu⁺ units along the main chain and has a 5-fold higher affinity than TEG–BA for trypsin, was inferior even to TEG–BA for trypsin inhibition.     

An aqueous molecular tube with polyaromatic frameworks capable of binding fluorescent dyes

An aqueous molecular tube composed of polyaromatic frameworks with peripheral hydrophilic groups was prepared. The new tube has a well-defined hydrophobic cavity with a diameter of ∼1 nm and quantitatively binds two molecules of fluorescent coumarin dyes in aqueous solutions. The bound coumarin dimers in a stacked fashion exhibit unusual excimer-like emissions in the confined space through efficient host–guest energy transfer.     

A convenient synthesis of 6-, 7-, and 8-membered cyclic phosphodiesters

1,3-, 1,4-, and 1,5-Alkanediols are converted into the corresponding 6-, 7-, and 8- membered cyclic phosphodiesters in a two-step procedure utilizing N-(1,2-dimethylethylene-dioxyphosphoryl)imidazole ($\text{2}\text{?}$ as the sole phosphorylating reagent.     

Luminescence switch-on detection of protein tyrosine kinase-7 using a G-quadruplex-selective probe

A series of luminescent iridium(iii) complexes were synthesised and evaluated for their ability to act as luminescent G-quadruplex-selective probes. The iridium(iii) complex 9 [Ir(pbi)₂(5,5-dmbpy)]PF₆ (where pbi = 2-phenyl-1H-benzo[d]imidazole; 5,5-dmbpy = 5,5′-dimethyl-2,2′-bipyridine) exhibited high luminescence for G-quadruplex DNA compared to dsDNA and ssDNA, and was employed to construct a G-quadruplex-based assay for protein tyrosine kinase-7 (PTK7) in aqueous solution. PTK7 is an important biomarker for a range of leukemias and solid tumors. In the presence of PTK7, the specific binding of the sgc8 aptamer sequence triggers a structural transition and releases the G-quadruplex-forming sequence. The formation of the nascent G-quadruplex structure is then detected by the G-quadruplex-selective iridium(iii) complex with an enhanced luminescent response. Moreover, the application of the assay for detecting PTK7 in cellular debris and membrane protein extract was demonstrated. To our knowledge, this is the first G-quadruplex-based assay for PTK7.