Terminal Alkyne-Modified DNA Aptamers with Enhanced Protein Binding Affinities

Nucleic acid-based receptors, known as aptamers, are relatively fast to discover and manufacture but lack the diverse functional groups of protein receptors (e.g., antibodies). The binding properties of DNA aptamers can be enhanced by attaching abiotic functional groups; for example, aromatic groups such as naphthalene slow dissociation from proteins. Although the terminal alkyne is a π-electron-rich functional group that has been used in small molecule drugs to enhance binding to proteins through noncovalent interactions, it remains unexplored for enhancing DNA aptamer binding affinity. Here, we demonstrate the utility of the terminal alkyne for improving the binding of DNA to proteins. We prepared a library of 256 terminal-alkyne-bearing variants of HD22, a DNA aptamer that binds the protein thrombin with nanomolar affinity. After a one-step thrombin-binding selection, a high-affinity aptamer containing two alkynes was discovered, exhibiting 3.2-fold tighter thrombin binding than the corresponding unmodified sequence. The tighter binding was attributable to a slower rate of dissociation from thrombin (5.2-fold slower than HD22). Molecular dynamics simulations with enhanced sampling by Replica Exchange with Solute Tempering (REST2) suggest that the π-electron-rich alkyne interacts with an asparagine side chain N-H group on thrombin, forming a noncovalent interaction that stabilizes the aptamer-protein interface. Overall, this work represents the first case of terminal alkynes enhancing the binding properties of an aptamer and underscores the utility of the terminal alkyne as an atom economical π-electron-rich functional group to enhance binding affinity with minimal steric perturbation.

Chloropentaphenyldisiloxane—Model Study on Intermolecular Interactions in the Crystal Structure of a Monofunctionalized Disiloxane

Small functional siloxane units have gained great interest as molecular model systems for mimicking more complex silicate structures both in nature and in materials chemistry. The crystal structure of chloropentaphenyldisiloxane, which was synthesized for the first time, was elucidated by single-crystal X-ray diffraction analysis. The molecular crystal packing was studied in detail using state-of-the-art Hirshfeld surface analysis together with a two-dimensional fingerprint mapping of the intermolecular interactions. It was found that the phenyl C–H bonds act as donors for both weak C–H···π and C–H···Cl hydrogen bond interactions. The influence of intramolecular Si–O–Si bond parameters on the acceptor capability of functional groups in intermolecular hydrogen bond interactions is discussed.

A Cyclic Periodic Wave Function Approach for the Study of Infinitely Periodic Solid-State Systems. I. Application to the C-H···π(C≡C) Hydrogen Bonding Systems

The cyclic periodic wave function (CPWF) approach is applied at the AM1 and PM3 semiempirical levels of approximation to infinitely periodic solid-state systems stabilized by weak CH-pi (C-H···π) interactions between repeat units. The reliability of the AM1 and PM3 methods for modeling C-H···π bonding is first demonstrated using two representative dimer systems: the T-shaped ethyne dimer and the T-shaped propyne dimer. The CPWF method is then applied to two different crystal systems that are stabilized by C-H···π interactions: (1) pent-4-ynoic acid solid and (2) a series of three infinite crystal systems-tetrakis(4-ethynylphenyl)methane solid, tetraethynylmethane solid, and tetrabutadiynylmethane solid. A comparison of our results with available data demonstrates that the use of the CPWF approach at the AM1 and PM3 levels of approximation provides a convenient and reliable method for the study of infinitely periodic systems containing very weak C-H···π bonding.

A thermostable glucose oxidase from Aspergillus heteromophus CBS 117.55 with broad pH stability and digestive enzyme resistance

In this study, the heterologous expression of an engineered thermostablle glucose oxidase from Aspergillus heteromophus CBS 117.55 was achieved in P. pastoris. This recombinant GoxAh was thermostable, with an optimal temperature range 25 °C-65 °C, and it was capable of retaining greater than 90% of its initial activity following a 10-min incubation at 75 °C. This enzyme had an optimum pH of 6.0, and it could retain above 80% of its initial activity following a 2-h incubation at a broad pH range (2.0-8.0). Moreover, GoxAh displayed excellent pepsin and trypsin resistance, and highly resistant to a range of tested metal ions and chemical reagents. These good properties make GoxAh a promising candidate for feed additive. The K_m and k_cat/K_m values of GoxAh were 187 mM and 1.09/mM/s, which limited its widespread application to some degree. However, due to its excellent characteristics, GoxAh is still of potential economic value for high value-added areas, as well as a good initial enzyme for developing applicable feed enzyme by protein engineering.

Some new nanostructure zinc complex: Synthesis, spectral analyses, crystal structure, Hirshfeld surface analyses, antimicrobial/anticancer, thermal behavior and usage as precursor for ZnO nanostructure

In this work, a new tridentate ligand, its some novel zinc halide/pseudohalide complexes and their antimicrobial and cytotoxic effects of them are described. Characterization data of these compounds have been achieved via several physical and micro analytical techniques. As typical one, X-ray crystal structure analysis of zinc azide complex was run showing zinc center is penta-coordinated by three nitrogen atoms from Schiff base ligand and two terminal azide nitrogen atoms as a distorted square pyramidal geometry. Hirshfeld surfaces analysis clears the important role of interactions related to azide groups (NH⋯N and CH⋯N hydrogen bonds) in the stabilization of its supramolecular structure. According to data obtained from thermal analysis (TG/DTG/DTA), all complexes are decomposed at four or more thermal stages below 1000 °C. Moreover antimicrobial activities of the compounds were screened against some gram positive and gram negative bacteria. Furthermore anticancer activities of the complexes were studied against MDA-MB468 and k562 as two cancer cell lines. In final, three zinc complexes were also synthesized in nano scale by sonochemical method and one of them was utilized as the precursor for preparation of nanostructure ZnO confirmed by XRD pattern and SEM image.

From Frustrated Packing to Tecton-Driven Porous Molecular Solids

Structurally divergent molecules containing bulky substituents tend to produce porous materials via frustrated packing. Two rigid tetrahedral cores, tetraphenylmethane and 1,3,5,7-tetraphenyladamantane, grafted peripherally with four (trimethylsilyl)ethynyl moieties, were found to have only isolated voids in their crystal structures. Hence, they were modified into tecton-like entities, tetrakis(4-(iodoethynyl)phenyl)methane [I4TEPM] and 1,3,5,7-tetrakis(4-(iodoethynyl)phenyl)adamantane [I4TEPA], in order to deliberately use the motif-forming characteristics of iodoethynyl units to enhance crystal porosity. I4TEPM not only holds increased free volume compared to its precursor, but also forms one-dimensional channels. Furthermore, it readily co-crystallizes with Lewis basic solvents to afford two-component porous crystals.

A [C1 + C2] route to propargylidyne complexes

The reactions of [W(CBr)(CO)₂(Tp*)] with a range of terminal alkynes (RCCH), mediated by [Pd(PPh₃)₄] and CuI, afford new propargylidynes [W(C–CCR)(CO)₂(Tp*)] [R = ^tBu, C₆H₄X (X = H, NH₂, NO₂), APh₃ (A = C, Si, Ge), B(O₂CCH₂)₂NMe].

Ho-Mediated Alkyne Reactions at Low Temperatures on Ag(111)

Low-temperature approaches to catalytic conversions promise efficiency, selectivity, and sustainable processes. Control over certain coupling reactions can be obtained via the pre-positioning of reactive moieties by self-assembly. However, in the striving field of on-surface synthesis atomistic precision and control remains largely elusive, because the employed coupling reactions proceed at temperatures beyond the thermal stability of the supramolecular templates. Here, utilizing scanning tunneling microscopy, we demonstrate terminal alkyne on-surface reactions mediated by Ho atoms at a weakly reactive Ag(111) substrate at low-temperatures. Density functional theory calculations confirm the catalytic activity of the involved adatoms. Pre-deposited Ho induces alkyne dehydrogenation starting at substrate temperatures as low as 100 K. Ho arriving at molecularly pre-covered surfaces held at 130 and 200 K produces covalent enyne-linked dimers and initiates cyclotrimerization, respectively. Statistical product analysis indicates a two-step pathway for the latter, whereby the enyne intermediates influence the distribution of the products. High chemoselectivity results from the absence of cyclotetramerization and diyne-forming homocoupling. Our analysis indicates that mainly the arriving Ho adatoms enable the coupling. These findings support the concept of dynamic heterogeneity by single-atom catalysts and pave the way for alternative means to control on-surface reactions.

Sonication-assisted synthesis of a new cationic zinc nitrate complex with a tetradentate Schiff base ligand: Crystal structure, Hirshfeld surface analysis and investigation of different parameters influence on morphological properties

A nanostructured cationic zinc nitrate complex with a formula of [ZnLNO₃]NO₃ (where L = (N²E,N^2'E)-N¹,N^1'-(ethane-1,2-diyl)bis(N²-((E)-3-phenylallylidene)ethane-1,2-diamine)) was prepared by sonochemical process and characterized by single crystal X-ray crystallography, scanning electron microscopy (SEM), FT-IR and NMR spectroscopy and X-ray powder diffraction (XRPD). The X-ray analysis demonstrates the formation of a cationic complex that metal center is five-coordinated by four nitrogen atom from Schiff base ligand and one oxygen atom from nitrate group. The crystal packing analysis demonstrates the essential role of the nitrate groups in the organization of supramolecular structure. The morphology and size of ultrasound-assisted synthesized zinc nitrate complex have been investigated using scanning electron microscopy (SEM) by changing parameters such as the concentration of initial reactants, the sonication power and reaction temperature. In addition the calcination of zinc nitrate complex in air atmosphere led to production of zinc oxide nanoparticles.

Mechanical Properties of Microcrystalline Metal-Organic Frameworks (MOFs) Measured by Bimodal Amplitude Modulated-Frequency Modulated Atomic Force Microscopy

Direct measurement of the mechanical properties of microcrystalline metal-organic framework (MOF) nanoparticles is challenging and rarely explored. In this work, we apply an effective method to realize elastic modulus mapping of a series of isostructural single MOF nanoparticles (100-500 nm) via bimodal amplitude modulated-frequency modulated atomic force microscopy. By probing five types of zirconium (Zr) and hafnium (Hf) isostructural UiO-66-type MOFs, we experimentally found that UiO-66(Hf)-type MOFs possess the higher elastic modulus (46-104 GPa) than that of UiO-66(Zr)-type MOFs (34-100 GPa), both of which are higher than that of reported zinc/copper based MOFs (3-10 GPa). We also experimentally demonstrate that the mechanical properties of MOFs can be tuned by adjusting the chemical functionalities of the ligands or using different metal nodes. In detail, the sterically bulky functional groups increase the mechanical properties of the resultant UiO-66-type MOFs, possibly due to the increased atomic density. These results pave a way to the direct measurement of mechanical properties of MOFs crystalline particles and provide an incisive perspective to the design of MOFs with high mechanical properties.

Acceptor properties of amino groups in aminobenzene crystals: study from the energetic viewpoint

The role of the N–H⋯N hydrogen bonds in the organization of the crystals of the aniline and diaminobenzenes has been studied.

Uncovering Intramolecular π-Type Hydrogen Bonds in Solution by NMR Spectroscopy and DFT Calculations

Reaction between the phosphinito bridged diplatinum species [(PHCy2 )Pt(μ-PCy2 ){κ(2) P,O-μ-P(O)Cy2 }Pt(PHCy2 )](Pt-Pt) (1), and (trimethylsilyl)acetylene at 273 K affords the σ-acetylide complex [(PHCy2 )(η(1) -Me3 SiC≡C)Pt(μ-PCy2 )Pt(PHCy2 ){κP-P(OH)Cy2 }](Pt-Pt) (2) featuring an intramolecular π-type hydrogen bond. Scalar and dipolar couplings involving the POH proton were detected by 2D NMR experiments. Relativistic DFT calculations of the geometry, relative energy, and NMR properties of model systems of 2 confirmed the structural assignment and allowed the energy of the π-type hydrogen bond to be estimated (ca. 22 kJ mol(-1) ).

Crystal structures, Hirshfeld surface analyses and thermal behavior of two new rare tetrahedral terminal zinc(ii) azide and thiocyanate Schiff base complexes

Crystal structures, Hirshfeld surface and thermal analyses of two new rare tetrahedral terminal zinc(ii) thiocyanate and azide Schiff base complexes of [ZnL(NCS)₂] and [ZnL(N₃)₂] are presented.

On-surface polymerization of 1,4-diethynylbenzene on Cu(111)

The polymerization of 1,4-diethynylbenzene was studied on a Cu(111) surface using scanning tunneling microscopy (STM) under ultra-high vacuum conditions. Thermal activation yielded disordered covalent networks, where distinct basic structural motifs indicate different coupling reactions.

On the Relevance of Considering the Intermolecular Interactions on the Prediction of the Vibrational Spectra of Isopropylamine

The effects of implicitly considering the effects of hydrogen bonding on the molecular properties, such as vibrational frequencies, were inferred on the basis of DFT calculations. Several clusters of isopropylamine were assembled and theoretically characterized. The results showed that maximum H-bond cooperativity is achieved when the amine group acts simultaneously as donor and acceptor. The effect of H-bond cooperativity manifests itself in the relative cluster stability and on the structural and vibrational frequency predictions. Referring to the vibrational frequencies it was found that theNH2stretching and torsion vibrational modes are the most affected by the amine involvement in hydrogen bonding. Both stretching modes were found to be significantly redshifted relative to the monomer. TheNH2torsional mode, on the other hand, was found to be blueshifted up to 350 cm-1. Finally, the comparative study between the theory levels performed allows to conclude that the small 6-31G* basis set is able to stabilize weakC–H⋯Ninteractions as long as the new dispersion corrected DFT methods are considered. The impairments observed with conventional DFT methods for describing weak interactions may be overcome with the improvement of basis set, but the associated increase of computational costs may turn the calculations unfeasible.

The basicity of unsaturated hydrocarbons as probed by hydrogen-bond-acceptor ability: bifurcated N-H+ ...pi hydrogen bonding

The competitive substitution of the anion (A(-)) in contact ion pairs of the type [Oct3NH+]B(C6F5)4 (-) by unsaturated hydrocarbons (L) in accordance with the equilibrium Oct3NH+...A(-) + nL right arrow over left arrow [Oct3NH+...Ln]A(-) has been studied in CCl4. On the basis of equilibrium constants, K, and shifts of nuNH to low frequency, it has been established that complexed Oct3NH...+Ln cations with n=1 and 2 are formed and have unidentate and bifurcated N--H+...pi hydrogen bonds, respectively. Bifurcated hydrogen bonds to unsaturated hydrocarbons have not been observed previously. The unsaturated hydrocarbons studied include benzene and methylbenzenes, fused-ring aromatics, alkenes, conjugated dienes, and alkynes. From the magnitude of the redshifts in the N--H stretching frequencies, Delta nuNH, a new scale for ranking the pi basicity of unsaturated hydrocarbons is proposed: fused-ring aromatics Collapse

Key Words

• bifurcated h-bonding
• ir spectroscopy
• π-basicity
• unsaturated hydrocarbons

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MESH Headings

• Hydrocarbons/chemistry
• Hydrogen/chemistry
• Hydrogen Bonding
• Molecular Structure
• Nitrogen Compounds/chemistry
• Solvents/chemistry
• Spectrophotometry, Infrared

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Grants

• R01 GM023851 NIGMS NIH HHS
• R01 GM023851-29 NIGMS NIH HHS
• GM 23851 NIGMS NIH HHS

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Affiliation(s)

Evgenii S. Stoyanov Department of Chemistry University of California, Riverside Riverside, California 92521, USA
Irina V. Stoyanova Department of Chemistry University of California, Riverside Riverside, California 92521, USA
Christopher A. Reed Department of Chemistry University of California, Riverside Riverside, California 92521, USA

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Metalloporphyrin-Based Inclusion Materials: Exploiting Ligating Topologies and Hydrogen-Bonding Backbones in Generating New Supramolecular Architectures

By coordination of the metal center of tetraphenylmetalloporphyrins (TPMP) [metal center=Zn(II) or Mn(II)] with pyridyl-based bidentate ligands, namely, N,N'-bis(4-pyridyl)urea (4BPU), N,N'-bis(3-pyridyl)urea (3BPU), and N-(4-pyridyl)isonicotinamide (4PIN), various axially modified tetraarylmetalloporphyrins (AMTAMPs) have been crystallographically characterized in their corresponding lattice inclusion complexes. Nine such inclusion crystals are prepared by crystallizing TPMP and the corresponding bidentate ligands in 1:2 molar ratio from suitable solvent systems. While the metal center Zn(II) of TPMP leads to the formation of both dimeric and monomeric AMTAMPs due to its preference for pentacoordinated geometry, the Mn(II) metal center of TPMP forms both polymeric and discrete hexacoordinated AMTAMPs due to its preference for hexacoordinated geometry. However, there seem to be no control on the formation of a particular AMTAMP. Structural analyses suggest that most of the AMTAMPs display new types of packing in the corresponding inclusion crystals.

The role of CH/pi interaction in the stabilization of less-soluble diastereomeric salt crystals

Enantiopure 2-naphthylglycolic acid (NGA) and cis-1-aminobenz[f]indan-2-ol (ABI) were rationally designed as new resolving agents on the model of mandelic acid (MA) and cis-1-aminoindan-2-ol (AI), respectively. As expected, NGA and ABI showed superior chiral recognition ability to racemates, compared with MA and AI. In order to clarify any factors governing the chiral recognition abilities of NGA and ABI, the crystal structures of their less- and more-soluble diastereomeric salts were determined by X-ray crystallographic analyses and revealed that CH/pi interactions play an intrinsic role in chiral recognitions. A theoretical investigation was also performed with the periodic ab initio method by using the X-ray crystal structures of the less-soluble salt crystals with AI and ABI to find the unique properties of CH/pi interaction in the crystalline state, which largely contributed to the stabilization of the crystals.

The World of Non-Covalent Interactions: 2006

The review focusses on the fundamental importance of non-covalent interactions in nature by illustrating specific examples from chemistry, physics and the biosciences. Laser spectroscopic methods and both ab initio and molecular modelling procedures used for the study of non-covalent interactions in molecular clusters are briefly outlined. The role of structure and geometry, stabilization energy, potential and free energy surfaces for molecular clusters is extensively discussed in the light of the most advanced ab initio computational results for the CCSD(T) method, extrapolated to the CBS limit. The most important types of non-covalent complexes are classified and several small and medium size non-covalent systems, including H-bonded and improper H-bonded complexes, nucleic acid base pairs, and peptides and proteins are discussed with some detail. Finally, we evaluate the interpretation of experimental results in comparison with state of the art theoretical models: this is illustrated for phenol...Ar, the benzene dimer and nucleic acid base pairs. A review with 270 references.