Superhydrophobic surfaces: are they really ice-repellent?

This work investigates the anti-ice performance of various superhydrophobic surfaces under different conditions. The adhesion strength of glaze ice (similar to that deposited during "freezing rain") is used as a measure of ice-releasing properties. The results show that the ice-repellent properties of the materials deteriorate during icing/deicing cycles, as surface asperities appear to be gradually damaged. It is also shown that the anti-icing efficiency of superhydrophobic surfaces is significantly lower in a humid atmosphere, as water condensation both on top of and between surface asperities takes place, leading to significantly larger values of ice adhesion strength. This work thus shows that superhydrophobic surfaces are not always ice-repellent and their use as anti-ice materials may therefore be limited.     

Distribution of N-glycosylation sequons in proteins: how apart are they?

N-glycosylation is a common protein modification process, which affects a number of properties of proteins. Little is known about the distribution of N-glycosylation sequons, for example, the distance between glycosylated sites and their position in the protein primary sequence. Using a large set of experimentally confirmed eukaryotic N-glycoproteins we analyzed the relative position and distribution of sequons. N-Glycosylation probability was found to be lower in the termini of protein sequences compared to the mid region. N-glycosylated sequons were found much farther from C terminus compared to the N-terminus of the protein sequence and this effect was more pronounced for NXS sequons. The distribution of sequons, modeled based on balls-in-boxes classical occupancy, showed a near-maximum probability. Considerable proportion of sequons was found within a distance of ten amino acids, indicating that the steric hindrance was not a key factor in protein N-glycosylation. Interestingly, the distribution of all sequons present in N-glycoproteins showed a pattern very similar to that of glycosylated sequons. The results indicate that protein N-glycosylation chiefly follows a random design.     

Carbohydrate-pi interactions: what are they worth?

Protein-carbohydrate interactions play an important role in many biologically important processes. The recognition is mediated by a number of noncovalent interactions, including an interaction between the alpha-face of the carbohydrate and the aromatic side chain of the protein. To elucidate this interaction, it has been studied in the context of a beta-hairpin in aqueous solution, in which the interaction can be investigated in the absence of other cooperative noncovalent interactions. In this beta-hairpin system, both the aromatic side chain and the carbohydrate were varied in an effort to gain greater insight into the driving force and magnitude of the carbohydrate-pi interaction. The magnitude of the interaction was found to vary from -0.5 to -0.8 kcal/mol, depending on the nature of the aromatic ring and the carbohydrate. Replacement of the aromatic ring with an aliphatic group resulted in a decrease in interaction energy to -0.1 kcal/mol, providing evidence for the contribution of CH-pi interactions to the driving force. These findings demonstrate the significance of carbohydrate-pi interactions within biological systems and also their utility as a molecular recognition element in designed systems.     

Manganese carbonyl fluorides: are they viable molecules?

The mononuclear Mn(CO)(5)X and binuclear Mn(2)(CO)(8)(μ-X)(2) manganese carbonyl halides have long been known for the halogens Cl, Br, and I. However, the corresponding manganese carbonyl fluorides (X = F) remain unknown. The structures and thermochemistry of such manganese carbonyl fluorides and their decarbonylation products have now been investigated using density functional theory. In all cases singlet structures were found to have lower energies than the corresponding triplet structures. The expected octahedral structure is predicted for Mn(CO)(5)F. Decarbonylation of Mn(CO)(5)F is predicted to give trigonal bipyramidal Mn(CO)(4)F with equatorial fluorine. Further, decarbonylation gives tetrahedral Mn(CO)(3)F. All of the binuclear Mn(2)(CO)(n)F(2) structures (n = 8, 7, 6) are predicted to have a central Mn(2)F(2) unit with two bridging F atoms, a non-bonding Mn···Mn distance of ~3.1 ?, and exclusively terminal CO groups. The thermochemistry of these manganese carbonyl fluorides indicates that they are viable species. This suggests that the failure to date to synthesize the simple manganese carbonyl fluorides arises from a lack of a suitable synthetic method rather than from the instability of the desired products.     

Anion-π aromatic neutral tweezers complexes: are they stable in polar solvents?

The impact of the solvent environment on the stabilization of the complexes formed by fluorine (T-F) and cyanide (T-CN) substituted tweezers with halide anions has been investigated theoretically. The study was carried out using computational methodologies based on density functional theory (DFT) and symmetry adapted perturbation theory (SAPT). Interaction energies were obtained at the M05-2X/6-31+G* level. The obtained results show a large stability of the complexes in solvents with large dielectric constant and prove the suitability of these molecular tweezers as potential hosts for anion recognition in solution. A detailed analysis of the effects of the solvent on the electron withdrawing ability of the substituents and its influence on the complex stability has been performed. In particular, the interaction energy in solution was split up into intermonomer and solvent-complex terms. In turn, the intermonomer interaction energy was partitioned into electrostatic, exchange, and polarization terms. Polar resonance structures in T-CN complexes are favored by polar solvents, giving rise to a stabilization of the intermonomer interaction, the opposite is found for T-F complexes. The solvent-complex energy increases with the polarity of the solvent in T-CN complexes, nonetheless the energy reaches a maximum and then decreases slowly in T-F complexes. An electron density analysis was also performed before and after complexation, providing an explanation to the trends followed by the interaction energies and their different components in solution.     

Ferrocene: Ironclad History or Rashomon Tale?

What really happened? To recount a pivotal 20th century chemical discovery, the assignment of its structure to ferrocene, ain't easy! One might have thought that telling the story would be straightforward, from published papers and correspondence with some of their authors. Not so. One emerges with a good bit of sympathy for historians of science-who did just what and why is pretty hard to determine, even when less than fifty years have elapsed.     

Protein and solvent dynamics: how strongly are they coupled?

Analysis of Raman and neutron scattering spectra of lysozyme demonstrates that the protein dynamics follow the dynamics of the solvents glycerol and trehalose over the entire temperature range measured 100-350 K. The protein's fast conformational fluctuations and low-frequency vibrations and their temperature variations are very sensitive to behavior of the solvents. Our results give insight into previous counterintuitive observations that protein relaxation is stronger in solid trehalose than in liquid glycerol. They also provide insight into the effectiveness of glycerol as a biological cryopreservant.     

Freely available conformer generation methods: how good are they?

Conformer generation has important implications in cheminformatics, particularly in computational drug discovery where the quality of conformer generation software may affect the outcome of a virtual screening exercise. We examine the performance of four freely available small molecule conformer generation tools (Balloon, Confab, Frog2, and RDKit) alongside a commercial tool (MOE). The aim of this study is 3-fold: (i) to identify which tools most accurately reproduce experimentally determined structures; (ii) to examine the diversity of the generated conformational set; and (iii) to benchmark the computational time expended. These aspects were tested using a set of 708 drug-like molecules assembled from the OMEGA validation set and the Astex Diverse Set. These molecules have varying physicochemical properties and at least one known X-ray crystal structure. We found that RDKit and Confab are statistically better than other methods at generating low rmsd conformers to the known structure. RDKit is particularly suited for less flexible molecules while Confab, with its systematic approach, is able to generate conformers which are geometrically closer to the experimentally determined structure for molecules with a large number of rotatable bonds (≥10). In our tests RDKit also resulted as the second fastest method after Frog2. In order to enhance the performance of RDKit, we developed a postprocessing algorithm to build a diverse and representative set of conformers which also contains a close conformer to the known structure. Our analysis indicates that, with postprocessing, RDKit is a valid free alternative to commercial, proprietary software.     

Biomedical applications of shape-memory polymers: howpractically useful are they?

Shape-memory effect (SME) is the ability of a material to change its dimension in a predefined way in response to an external stimulus. Polymers that exhibit SME are an important class of materials in medicine, especially for minimally invasive deployment of devices. However, the rate of translation of the concept to approved products is extremely low, with mostly nitinolbased devices being approved. In this review, the general aspects of the different types of stimuli that can be used to activate SME are reviewed and sterilization issues of shape-memory polymer (SMP)-based medical devices are addressed. In addition, the general usefulness as well as the limitations of the shape-memory effect for biomedical applications are described.     

Polyene photoisomerization rates: are they distinct in aqueous block copolymer micellar solutions and gels?

Photoisomerization of 3,3'-diethyloxadicarbocyanine iodide (DODCI) has been investigated in water, 5% and 30% aqueous triblock copolymer, poly(ethylene oxide)20-poly(propylene oxide)70-poly(ethylene oxide)20 (P123) by measuring the fluorescence quantum yields and lifetimes in the temperature range 293-318 K. Reports available in literature indicate that 5% aqueous P123 exists as micellar solution, whereas 30% aqueous P123 forms gel due to micelle-micelle entanglement. This study has been undertaken to find out how the polyene photoisomerization rates are influenced in the sol and gel phases. It has been observed that 60%-70% of DODCI is located in the palisade layer of the micelles in the sol as well as gel phases and the photoisomerization rate of this component is identical in both the phases at a particular temperature. The remainder of the probe is located in the interfacial region and isomerization rates of this fraction are slower by a factor of 1.4-1.1 in the gel phase compared with the micellar solution. The retardation of the isomerization rate in the gel phase has been explained on the basis of enhancement in the friction experienced by the probe due to micelle-micelle entanglement at the interface. Compared to the isomerization rates in water, the rates of photoisomerization of DODCI located in the palisade layer, interfacial region of micellar solution, and interfacial region of the micelles in the gel phase are slower by factors of 3.5, 1.5-1.9, and 2, respectively. The outcome of this study validates the point that in organized media photoisomerization rates are sensitive to the localized friction, which is not uniform unlike in a homogeneous solution.     

Fulvenes, fulvalenes, and azulene: are they aromatic chameleons?

On the basis of the theory of Baird on reversal of Hückel's rule for aromaticity and antiaromaticity of annulenes when going from the electronic ground state (S0) to the lowest pipi* triplet state (T1) (J. Am. Chem. Soc. 1972, 94, 4941), we argue that fulvenes, fulvalenes, and azulene are "aromatic chameleons". The dipole moments of fulvenes in T1 should be of comparable magnitude to those of S0, but due to the reversal of Hückel's aromaticity rule in T1, their dipole should be in the opposite direction. Thereby, they are capable of adopting some aromaticity in both the T1 and S0 states as they adapt their dipolar resonance structures. The same applies to fulvalenes and azulene in their lowest quintet states (Q1) when compared to S0. Our hypothesis on chameleon behavior is supported by quantum chemical OLYP, CASSCF, and CASPT2 calculations of dipole moments, pi-orbital populations, and energies.     

Looking at long molecules in solution: what happens when they are subjected to Couette flow?

Knowing the structure of a molecule is one of the keys to deducing its function in a biological system. However, many biomacromolecules are not amenable to structural characterisation by the powerful techniques often used namely NMR and X-ray diffraction because they are too large, or too flexible or simply refuse to crystallize. Long molecules such as DNA and fibrous proteins are two such classes of molecule. In this article the extent to which flow linear dichroism (LD) can be used to characterise the structure and function of such molecules is reviewed. Consideration is given to the issues of fluid dynamics and light scattering by such large molecules. A range of applications of LD are reviewed including (i) fibrous proteins with particular attention being given to actin; (ii) a far from comprehensive discussion of the use of LD for DNA and DNA-ligand systems; (iii) LD for the kinetics of restriction digestion of circular supercoiled DNA; and (iv) carbon nanotubes to illustrate that LD can be used on any long molecules with accessible absorption transitions.     

Linear C(n) clusters: are they acetylenic or cumulenic?

Uncapped linear Cn clusters have been studied with hybrid density functional theory focusing on the geometry, HOMO-LUMO gap, and the longitudinal optical (LO) vibrational mode. The latter two correlate well with the bond length alternation (BLA) of the optimized geometry. Due to end effects, the BLA is not constant along the chains. The degree of BLA changes continuously with increasing n: starting with essentially nonalternating structures (cumulenic), then turning into strongly alternating (acetylenic) structures. This transition has not yet been described or characterized and occurs at relatively large values of n. The implications for the widely observed characteristic LO vibrational bands of linear carbon clusters are discussed.     

Dimeric palladium complexes with bridging aryl groups: when are they stable?

Stable dimeric palladium(II) complexes of general formula [Pd(2)(mu-R)(2)(eta(3)-allyl)(2)] (R=haloaryl, mesityl) have been prepared. Their X-ray crystal structures, determined for some of the complexes, show that the two coordination square planes are usually coplanar. The haloaryl complexes are fluxional in solution, showing exchange between cis and trans isomers (relative to the orientation of the two allyl groups in the dimer) through solvent-assisted associative bridge splitting. A number of other ancillary ligands (O,O, S,S, or C,N donors) failed to stabilize the bridging situation. Also, bridging phenyls were unstable. The reasons for this behavior and the formation of alternative compounds in attempts at synthesizing them are fully analyzed and explained. Stable aryl bridges seem to be favored by a combination of factors: the use of ancillary ligands of small size and lacking electron lone pairs, and the use of aryl ligands reluctant to homo and hetero C--C coupling. These seem to be more important factors in the stabilization of bridging aryl complexes than the strength of the bridges themselves.     

Lead-like, drug-like or “Pub-like”: how different are they?

Academic and industrial research continues to be focused on discovering new classes of compounds based on HTS. Post-HTS analyses need to prioritize compounds that are progressed to chemical probe or lead status. We report trends in probe, lead and drug discovery by examining the following categories of compounds: 385 leads and the 541 drugs that emerged from them; "active" (152) and "inactive" (1488) compounds from the Molecular Libraries Initiative Small Molecule Repository (MLSMR) tested by HTS; "active" (46) and "inactive" (72) compounds from Nature Chemical Biology (NCB) tested by HTS; compounds in the drug development phase (I, II, III and launched), as indexed in MDDR; and medicinal chemistry compounds from WOMBAT, separated into high-activity (5,784 compounds with nanomolar activity or better) and low-activity (30,690 with micromolar activity or less). We examined Molecular weight (MW), molecular complexity, flexibility, the number of hydrogen bond donors and acceptors, LogP-the octanol/water partition coefficient estimated by ClogP and ALOGPS), LogSw (intrinsic water solubility, estimated by ALOGPS) and the number of Rule of five (Ro5) criteria violations. Based on the 50% and 90% distribution moments of the above properties, there were no significant difference between leads of known drugs and "actives" from MLSMR or NCB (chemical probes). "Inactives" from NCB and MLSMR were also found to exhibit similar properties. From these combined sets, we conclude that "Actives" (569 compounds) are less complex, less flexible, and more soluble than drugs (1,651 drugs), and significantly smaller, less complex, less hydrophobic and more soluble than the 5,784 high-activity WOMBAT compounds. These trends indicate that chemical probes are similar to leads with respect to some properties, e.g., complexity, solubility, and hydrophobicity.