A Molecular modeling study of the changes of some steric properties of the precatalysts during the olefin metathesis reaction

The productive self‐metathesis of 1‐octene with a series of new phosphine ligated Grubbs‐type precatalysts was studied. The resulting structures were used to compare some steric properties of the new precatalysts with those of well‐known precatalysts. The possibility of α‐CC agnostic stabilization as well as the ability of the ligands to shield the metal was studied. A comparison of the obtained data, pointed to the unlikelihood that α‐CC agostic stabilization is a major contribution to the stabilization of the various metallacyclobutane rings. The similarity in the ability of the ligands to shield the metal also raised questions about the comparison of experimentally observed trends with those obtained theoretically. © 2014 Wiley Periodicals, Inc.     

Osmotically Driven Formation of Double Emulsions Stabilized by Amphiphilic Block Copolymers

Double emulsions are valuable for the formation of multi‐compartmental structures. A variety of pathways to prepare double emulsions have been developed, but high‐throughput routes to droplets of controlled size and architecture remain scarce. A new single‐step process is introduced for preparation of water‐in‐oil‐in‐water double emulsions by a previously unexplained process of self‐emulsification. We show that the origin of this process is the osmotic stress resulting from the presence of salt impurities within the amphiphilic block copolymers used for emulsion stabilization. Further, we utilize osmotically driven emulsification to tailor the structures of multiple emulsions, which upon solvent evaporation can yield multi‐compartmental capsules or hierarchically structured porous films.     

Stabilization and growth of non-native nanocrystals at low and atmospheric pressures

The stabilization and growth of nanocrystals in "non-native" structures is explored via density functional calculations. Non-native and "native" bulk structures differ in their discrete translational symmetry. Computations suggest that the lower surface energy of the non-native structures always facilitates their stabilization in the early stages of crystal growth. In the compound semiconductors considered here, the transition pathways between non-native and native structures involve planar or near-planar depolarized layers and the growth conditions have significant effects on the stabilization and growth of non-native structures. The findings of this study help in identifying heuristics for the synthesis of non-native nanocrystals.     

Microstructural evolution in polyacrylonitrile fibers during oxidative stabilization

Microstructural evolution in polyacrylonitrile fibers during oxidative stabilization was investigated by high‐resolution transmission electron microscopy and wide‐angle X‐ray diffraction. Nanocrystallites and two types of amorphous structures, that is, onion‐like spheres and maze‐like matrix, are observed not only in the precursor fibers but also in the fibers stabilized at 230, 255, and 275 °C. During oxidative stabilization, changes take place earlier in the amorphous onion‐like spheres than in the ordered regions. With increasing temperature, the outer layers of the onion‐like spheres gradually interlace with each other, microscopically demonstrating crosslinking reactions among neighboring macromolecules. The interplanar spacing in crystalline regions increases and the crystallite size decreases as a result of an order–disorder transition. The transition in large crystallites is not completed even in the fibers that are stabilized at 275 °C, suggesting that uniform microstructure and fine crystallites are conducive to homogenous stabilization. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 759–765, 2008     

Stabilization of zwitterionic proline by DMSO

Zwitterionic stabilization and metal‐free organocatalysis are two emerging topics. In this work, the numbers of DMSO molecules required to render zwitterionic proline geometrically stable, energetically preferential, and conformationally predominant have been determined, as one, three, and three, respectively. Conformations are analyzed for proline conformers interacted with one, two, and three DMSO molecules, and three DMSO molecules are enough to fill up the first shell of proline. Relative stabilities of two selected canonical structures are dependent on the DMSO contents, while zwitterionic stabilities improve monotonously with increase of DMSO contents. DMSO causes a conformational diversity and good zwitterionic stabilization effects, which result from the synergetic effects of two types of H‐bonding interactions. With increase of DMSO contents, type‐2 H‐bonding (CH as donors) contributes more to zwitterionic stabilization. At any DMSO content, zwitterionic proline is facile to form because of low activation energies, and this study helps to understand proline‐catalyzed processes. © 2015 Wiley Periodicals, Inc.     

Effects of Six‐Membered Carbohydrate Rings on Structure,Stability, and Kinetics of G‐Quadruplexes

We have evaluated the conformational, thermal, and kinetic properties of d(TGGGGT) analogues with one or five of the ribose nucleotides replaced with the carbohydrate residues hexitol nucleic acid (HNA), cyclohexenyl nucleic acid (CeNA), or altritol nucleic acid (ANA). All of the modified oligonucleotides formed G‐quadruplexes, but substitution with the six‐membered rings resulted in a mixture of G‐quadruplex structures. UV and CD melting analyses showed that the structure formed by d(TGGGGT) modified with HNA was stabilized whereas that modified with CeNA was destabilized, relative to the structure formed by the unmodified oligonucleotide. Substitution at the fourth base of the G‐tract with ANA resulted in a greater stabilization effect than substitution at the first G residue; substitution with five ANA residues resulted in significant stabilization of the G‐quadruplex. A single substitution with CeNA at the first base of the G‐tract or five substitutions with HNA resulted in striking deceleration or acceleration of G‐quadruplex formation, respectively. Our results shed light on the effect of the sugar moiety on the properties of G‐quadruplex structures.     

Interaction of aromatic units of amino acids with guanidinium cation: The interplay of π···π, XH···π, and M+···π contacts

Complexes formed by guanidinium cation and a pair of aromatic molecules among benzene, phenol, or indole have been computationally studied to determine the characteristics of the cation···π interaction in ternary systems modeling amino acid side chains. Guanidinium coordinates to the aromatic units preferentially in the following order: indole, phenol, and benzene. Complexes containing two different aromatic units show an intermediate behavior between that observed for complexes with only one kind of aromatic unit. Most stable structures correspond to doubly‐T shaped arrangements with the two aromatic units coordinating guanidinium by its NH₂ groups. Other structures with only one aromatic unit coordinated to guanidinium, such as T‐shaped or parallel‐stacked ones, are less favorable but still showing significant stabilization. In indole and phenol complexes, the formation of hydrogen bonds between the aromatic molecules introduces extra stabilization in T‐shaped structures. Three body effects are small and repulsive in doubly T‐shaped minima. Only when hydrogen bonds involving the aromatic molecules are formed in T‐shaped structures a cooperative effect can be observed. In most complexes the interaction is controlled by electrostatics, with induction and dispersion also contributing significantly depending on the nature and orientation of the aromatic species forming the complex. Although the stability in these systems is mainly controlled by the intensity of the interaction between guanidinium and the aromatic molecules coordinated to it, interactions between aromatic molecules can modulate the characteristics of the complex, especially when hydrogen bonds are formed. © 2014 Wiley Periodicals, Inc.     

Ion‐Responsive Hemin–G‐Quadruplexes for Switchable DNAzyme and Enzyme Functions

Programmed nucleic acid sequences undergo K⁺ ion‐induced self‐assembly into G‐quadruplexes and separation of the supramolecular structures by the elimination of K⁺ ions by crown ether or cryptand ion‐receptors. This process allows the switchable formation and dissociation of the respective G‐quadruplexes. The different G‐quadruplex structures bind hemin, and the resulting hemin–G‐quadruplex structures reveal horseradish peroxidase DNAzyme catalytic activities. The following K⁺ ion/receptor switchable systems are described: 1) The K⁺‐induced self‐assembly of the Mg²⁺‐dependent DNAzyme subunits into a catalytic nanostructure using the assembly of G‐quadruplexes as bridging unit. 2) The K⁺‐induced stabilization of the anti‐thrombin G‐quadruplex nanostructure that inhibits the hydrolytic functions of thrombin. 3) The K⁺‐induced opening of DNA tweezers through the stabilization of G‐quadruplexes on the “tweezers’ arms" and the release of a strand bridging the tweezers into a closed structure. In all of the systems reversible, switchable, functions are demonstrated. For all systems two different signals are used to follow the switchable functions (fluorescence and the catalytic functions of the derived hemin–G‐quadruplex DNAzyme).     

Constrained Peptides with Target‐Adapted Cross‐Links as Inhibitors of a Pathogenic Protein–Protein Interaction

Bioactive conformations of peptides can be stabilized by macrocyclization, resulting in increased target affinity and activity. Such macrocyclic peptides proved useful as modulators of biological functions, in particular as inhibitors of protein–protein interactions (PPI). However, most peptide‐derived PPI inhibitors involve stabilized α‐helices, leaving a large number of secondary structures unaddressed. Herein, we present a rational approach towards stabilization of an irregular peptide structure, using hydrophobic cross‐links that replace residues crucially involved in target binding. The molecular basis of this interaction was elucidated by X‐ray crystallography and isothermal titration calorimetry. The resulting cross‐linked peptides inhibit the interaction between human adaptor protein 14‐3‐3 and virulence factor exoenzyme S. Taking into consideration that irregular peptide structures participate widely in PPIs, this approach provides access to novel peptide‐derived inhibitors.     

Strategies toward well‐defined polymer nanoparticles inspired by nature: Chemistry versus versatility

Polymeric nanoparticles are promising delivery platforms for various biomedical applications. One of the main challenges toward the development of therapeutic nanoparticles is the premature disassembly and release of the encapsulated drug. Among the different strategies to enhance the kinetic stability of polymeric nanoparticles, shell‐ and core‐crosslinking have been shown to provide robust character, while creating a suitable environment for encapsulation of a wide range of therapeutics, including hydrophilic, hydrophobic, metallic, and small and large biomolecules, with gating of their release as well. The versatility of shell‐ and core‐crosslinked nanoparticles is driven from the ease by which the structures of the shell‐ and core‐forming polymers and crosslinkers can be modified. In addition, postmodification with cell‐recognition moieties, grafting of antibiofouling polymers, or chemical degradation of the core to yield nanocages allow the use of these robust nanostructures as “smart” nanocarriers. The building principles of these multifunctional nanoparticles borrow analogy from the synthesis, supramolecular assembly, stabilization, and dynamic activity of the naturally driven biological nanoparticles such as proteins, lipoproteins, and viruses. In this review, the chemistry involved during the buildup from small molecules to polymers to covalently stabilized nanoscopic objects is detailed, with contrast of the strategies of the supramolecular assembly of polymer building blocks followed by intramicellar stabilization into shell‐, core‐, or core–shell‐crosslinked knedel‐like nanoparticles versus polymerization of polymers into nanoscopic molecular brushes followed by further intramolecular covalent stabilization events. The rational design of shell‐crosslinked knedel‐like nanoparticles is then elaborated for therapeutic packaging and delivery, with emphasis on the polymer chemistry aspects to accomplish the synthesis of such nanoparticulate systems. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5'-d(GCGAAGC)-3' hairpin: Complete basis set calculations at the MP2 and CCSD(T) levels

Stabilization energies of the H-bonded and stacked structures of a DNA base pair were studied in the crystal structures of adenine-thymine, cytosine-guanine, and adenine-cytosine steps as well as in the 5'-d(GCGAAGC)-3' hairpin (utilizing the NMR geometry). Stabilization energies were determined as the sum of the complete basis set (CBS) limit of MP2 stabilization energies and the Delta E(CCSD(T)) - Delta E(MP2) correction term evaluated with the 6-31G*(0.25) basis set. The CBS limit was determined by a two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T. While the H-bonding energies are comparable to those of base pairs in a crystal and a vacuum, the stacking energies are considerably smaller in a crystal. Despite this, the stacking is still important and accounts for a significant part of the overall stabilization. It contributes equally to the stability of DNA as does H-bonding for AT-rich DNAs, while in the case of GC-rich DNAs it forms about one-third of the total stabilization. Interstrand stacking reaches surprisingly large values, well comparable to the intrastrand ones, and thus contributes significantly to the overall stabilization. The hairpin structure is characterized by significant stacking, and both guanine...cytosine pairs possess stacking energies larger than 11.5 kcal/mol. A high portion of stabilization in the studied hairpin comes from stacking (similar to that found for AT-rich DNAs) despite the fact that it contains two GC Watson-Crick pairs having very large H-bonding stabilization. The DFT/B3LYP/6-31G** method yields satisfactory values of interaction energies for H-bonded structures, while it fails completely for stacking.     

Assessing G4-Binding Ligands In Vitro and in Cellulo Using Dimeric Carbocyanine Dye Displacement Assay

G-quadruplexes (G4) are the most actively studied non-canonical secondary structures formed by contiguous repeats of guanines in DNA or RNA strands. Small molecule mediated targeting of G-quadruplexes has emerged as an attractive tool for visualization and stabilization of these structures inside the cell. Limited number of DNA and RNA G4-selective assays have been reported for primary ligand screening. A combination of fluorescence spectroscopy, AFM, CD, PAGE, and confocal microscopy have been used to assess a dimeric carbocyanine dye B6,5 for screening G4-binding ligands in vitro and in cellulo. The dye B6,5 interacts with physiologically relevant DNA and RNA G4 structures, resulting in fluorescence enhancement of the molecule as an in vitro readout for G4 selectivity. Interaction of the dye with G4 is accompanied by quadruplex stabilization that extends its use in primary screening of G4 specific ligands. The molecule is cell permeable and enables visualization of quadruplex dominated cellular regions of nucleoli using confocal microscopy. The dye is displaced by quarfloxin in live cells. The dye B6,5 shows remarkable duplex to quadruplex selectivity in vitro along with ligand-like stabilization of DNA G4 structures. Cell permeability and response to RNA G4 structures project the dye with interesting theranostic potential. Our results validate that B6,5 can serve the dual purpose of visualization of DNA and RNA G4 structures and screening of G4 specific ligands, and adds to the limited number of probes with such potential.     

Synthesis,crystal structures,spectral FT‐IR,NMR and UV–Vis investigations and Hirshfeld surface analysis of two new 2‐hydroxyethyl‐substituted N‐heterocyclic carbene precursors

This study discusses the synthesis of two new 2‐hydroxyethyl substituted N‐heterocyclic carbene (NHC) precursors. The NHC precursors were prepared from 1‐(alkyl/aryl)benzimidazole and alkyl halides. They were characterized using ¹H NMR, ¹³C NMR, FT‐IR, UV–Vis spectroscopy, and elemental analysis techniques. Molecular and crystal structures of 1 and 2 were determined using the single‐crystal X‐ray diffraction method. Crystal structure of the compounds features NHC precursors and chloride anions. Additionally in 2 , the asymmetric unit has a water molecule, which forms a tetrameric chloride‐hydrate assembly with the chloride anion. The chloride anions play an important role in the stabilization of crystal structures to form a two‐dimensional supramolecular architecture. The 3D Hirshfeld surface and the associated 2D fingerprint plots were also drawn to gain insights into the behavior of the interactions in the compounds.     

Designer peptide surfactants stabilize diverse functional membrane proteins

Multi-spanning integral membrane proteins, including G-protein coupled receptors (GPCR), ion channels, and ion transporters, comprise a major class of drug targets. However, despite their vital importance, most molecular structures of membrane proteins remain elusive. This is largely due to lack of effective materials and methods to stabilize their functional conformation for sufficient time. Thus finding optimal surfactants and developing new approaches to study fundamental properties of unstable membrane proteins is urgently needed. In this tutorial review we summarize designer peptides with surfactant properties and their usefulness to stabilize membrane proteins. These peptide surfactants present new opportunities for the stabilization and characterization of diverse membrane proteins. Previous studies on the interaction between surfactant peptides and membrane proteins revealed strategies to design new peptides tailor-made for the stabilization of specific proteins. We review examples of solubilization, purification, long-term stabilization of membrane proteins, and the design principles of peptide sequences. We discuss future trends for exploiting spatial features, thermodynamic parameters, and self-assembling properties to create peptide surfactant structures to facilitate the characterization of diverse membrane proteins.     

Clustering of nucleobases with alkali metals studied by electrospray ionization tandem mass spectrometry: implications for mechanisms of multistrand DNA stabilization

Self-clustering of the five common nucleobases was investigated by electrospray ionization tandem mass spectrometry and shown to provide insight into the non-covalent interactions between identical bases. Alkali and ammonium cations significantly increase self-aggregation of the nucleobases and lead to the formation of uniquely stable magic number clusters. Sodium adducts of guanine, thymine and uracil preferentially take the form of tetrameric (quartet) clusters. This gas-phase result correlates with previously reported solution-phase data on sodium cation stabilized guanosine, thymine and uracil quartet structures believed to be responsible for telomere stabilization. In the presence of potassium, cesium or ammonium cations, pentameric magic number clusters are formed from thymine and uracil, while in solution the nucleoside isoguanosine yields clusters of this favored size. The formation of magic number metaclusters occurs for thymine and uracil in the presence of ammonium cations. These doubly charged 10- and 15-mers are tentatively attributed to the formation of pentamer/ammonium cation/ pentamer sandwich structures.     

Synthesis, molecular and electronic structures of six-coordinate transition metal (Mn, Fe, Co, Ni, Cu, and Zn) complexes with redox-active 9-hydroxyphenoxazin-1-one ligands

A series of pseudo-octahedral metal (M = Mn, Fe, Co, Ni, Cu, Zn) complexes 4 of a new redox-active ligand, 2,4,6,8-tetra(tert-butyl)-9-hydroxyphenoxazin-1-one 3, have been synthesized, and their molecular structures determined with help of X-ray crystallography. The effective magnetic moments of complexes 4 (M = Mn, Fe, Co, and Ni) measured in the solid state and toluene solution point to the stabilization of their high-spin electronic ground states. Detailed information on the electronic structure of the complexes and their redox-isomeric forms has been obtained using density functional theory (DFT) B3LYP*/6-311++G(d,p) calculations. The energy disfavored low-spin structures of manganese, iron, and cobalt complexes have been located, and based on the computed geometries and distribution of spin densities identified as Mn(IV)[(Cat-N-SQ)](2), Fe(II)[Cat-N-BQ)](2), and Co(II)[Cat-N-BQ)](2) compounds, respectively. It has been shown that stabilization of the high-spin structures of complexes 4 (M = Mn, Fe, Co) is caused by the rigidity of the molecular framework of ligands 3 that sterically inhibits interconversions between the redox-isomeric forms of the complexes. The calculations performed on complex 4 (M = Co) predict that a suitable structural modification that might provide for stabilization of the low-spin electromeric forms and create conditions for the valence tautomeric rearrangement via stabilization of the low-spin electromer and narrowing energy gap between the low-spin ground state tautomer and the minimal energy crossing point on the intersection of the potential energy surfaces of the interconverting structures consists in the replacement of an oxygen in the oxazine ring by a bulkier sulfur atom.     

Stabilization of boron clusters with classical fullerene structures by combined doping effect: a quantum chemical study

A combined approach (endohedral doping and exohedral environment) to stabilization of boron clusters with classical fullerene structures has been studied. The boron clusters with classical fullerene structures are stable when heteroatomic part of the complex (endohedral atom and exohedral environment) donates in total 18 electrons to the composite system, stability of which depends on the coordination capabilities and donor ability of the endohedral and surrounding atoms. The most effective stabilization is achieved in the case of the endohedral transition metals atoms, whereas the most effective environment is given by the lithium surrounding.

     

Shell crosslinked polymer assemblies: Nanoscale constructs inspired from biological systems

The general approach involving the organization of polymers into micellar assemblies followed by stabilization through covalent intramicellar crosslinking of the assemblies has emerged as a powerful method for the production of well‐defined nanostructured materials, having an amphiphilic core‐shell morphology. When the covalent crosslinks are limited to the chain segments that compose the polymer micelle shell, then shell crosslinked knedel‐like (SCK) nanostructures result. The shell composition dictates the interactions of the SCKs with external agents, forms a barrier layer over the core domain, and provides robust character to the nanoparticle. Because of the stability that the crosslinked shell provides, the core domain can be of dramatically different compositions and properties—glassy, fluidlike, and crystalline polymer chains have been employed for the core material and the effects that each contributes to the overall nanostructure properties have been examined. Most notably, the shell crosslinks allow for complete removal of the core to generate hollow (solvent‐filled) nanoscale cagelike structures. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 1397–1407, 2000     

Conformational influence on the type of stabilization of sulfur radical cations in cyclic peptides.

The free-radical chemistry of two oxidized cyclic dipeptides is investigated using time-resolved optical and conductivity detection. Two cyclic dipeptides, cyclo-Gly-L-Met and cyclo-D-Met-L-Met, are synthesized and irradiated with nanosecond pulses of electrons, which initiate the oxidation of the methionine side chains with hydroxyl radicals from the radiolysis of water. The cyclic peptides are taken to be models for the interior of proteins where there are no terminal groups. This opens up the possibility that neighboring-group effects can be studied directly between the initially formed sulfur radical cations and the heteroatoms associated with the peptide bonds. Such complexation of the sulfur radical cations is observed with the amide nitrogen atoms. In addition, intermolecular stabilization with the unoxidized sulfur atoms on separate cyclic dipeptide molecules is observed. Little or no intramolecular stabilization by the unoxidized sulfur in the neighboring methionine occurs in cyclo-D-Met-L-Met, in contrast to the previously observed intramolecular sulfur stabilization of the sulfur radical cation in the isomer cyclo-L-Met-L-Met. This contrasting behavior is rationalized by conformational differences in the two isomers as seen through molecular-modeling simulations. The implications for the oxidation of the protein calmodulin, which contains multiple residues of methionine, are discussed as having analogous determining factors.     

分散剂分子结构特征对煤浆流变特性的影响

系统考察了具有不同分子结构特片系列分散剂对高浓度煤浆性质的影响。发现煤的成浆性、浆体的流变特性和稳定化作用与分散剂的分子结构特征密切相关。就本研究所涉及的分散剂种类和煤种而言，分散剂单体结构中多核芳烃结构所占比例较小时易于使浆体呈屈服假塑性，相反，则使浆体呈屈服胀塑性。分散剂单体的侧链结构对煤成浆性和浆体流变性的影响不很突出，而分散剂的第二单体结构的影响却非常显著。结果还同时表明，分散剂的高分散性能是导致浆体呈屈服胀塑性流体和弱化浆体稳定化作用的重要因素。