Self-sorting: the exception or the rule?

In this paper, we pose the question of whether self-sorting in designed systems is exceptional behavior or whether it is likely to become a more general phenomenon governing molecular recognition and self-assembly. To address this question we prepared a mixture comprising two of Davis' self-assembled ionophores, Rebek's tennis ball and calixarene tetraurea capsule, Meijer's ureidopyrimidinone, Reinhoudt's calixarene bis(rosette), and two molecular clips in CDCl(3) solution and observed the behavior of this ensemble by (1)H NMR. As hypothesized, high-fidelity self-sorting behavior was observed. The influence of several key variables-temperature, concentration, equilibrium constants, and the presence of competitors-on the fidelity of self-sorting is described. These results show that self-sorting is neither the exception nor the rule. They suggest, however, that the subset of known molecular aggregates that exceed the criteria required for thermodynamic self-sorting is larger than previously appreciated and potentially quite broad.     

Structure and bonding in the isoelectronic series CnHnP5-n+: is phosphorus a carbon copy?

The relative stabilities of different isomers of the isoelectronic series C(n)H(n)P(5-n)(+) have been investigated using G3X theory. The results indicate that all species containing one or more phosphorus atom adopt a three-dimensional nido geometry, in marked contrast to the planar structure favoured by the all-carbon analogue. Within isomeric nido clusters, a strong correlation between total energy and the nucleus-independent chemical shift (NICS) indicates that three-dimensional aromaticity plays a significant role in determining the stability of the cluster. In the context of these nido clusters, the extent to which phosphorus is a carbon copy proves to be highly dependent on the global electronic environment. The first isolobal substitution of CH by P causes a complete switch from localised to delocalised bonding, accompanied by a transition from a two- to a three-dimensional structure, with the phosphorus atom showing a strong preference for the unique apical site. In contrast, further increasing the phosphorus content causes no further change in structure or bonding, suggesting that, at the basal sites, phosphorus is a rather better carbon copy. The low-energy pathways for interconversion of apical and basal atoms previously identified in C(2)H(2)P(3)(+) prove to be a general feature of all members of the series.     

Concerning the question of covalent bonding in hypericin-chromoproteins: Schiff base formation?

Summary Depending on the reaction conditions,peri-hydroxy substituted anthraquinones like 1,8-dihydroxyanthraquinone and 1,4-dihydroxyanthraquinone could be derivatized with ammonia, propylamine, isopropylamine, and a lysine derivative to yield a variety of imino and amino substitution and addition products. However, hypericin resisted such derivatization under a variety of reaction conditions. Therefore, the hypothesis that hypericin is bound to its apoprotein in photopigmentsvia a Schiff base to the -amino group of a lysine residue or a terminal amino group seems to be rather unlikely.

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Zur Frage der kovalenten Bindung in Hypericin-Chromoproteiden: Schiff-Basenbildung?

Zusammenfassung Abhängig von den Reaktionsbedingungen gabenperi-hydroxylsubstituierte Anthrachinone, wie 1,8-Dihydroxyanthrachinon oder 1,4-Dihydroxyanthrachinon, mit Propylamin, Isopropylamin und einem Lysinderivat eine Reihe von Imino- und Amino-Substitutionsprodukten oder Addukten. Allerdings widerstand Hypericin unter Variation der Reaktionsbedingungen einer solchen Derivatisierung. Deshalb ist die Hypothese, daß Hypericin in seinen Photopigmenten über eine Schiffsche Base mit der -Aminogruppe eines Lysinrestes oder mit einer terminalen Aminogruppe verknüpft ist, eher unwahrscheinlich.

     

From symmetry breaking to symmetry swapping: is Kasha's rule violated in multibranched phenyleneethynylenes?

The phenomenon of excited-state symmetry breaking is often observed in multipolar molecular systems, significantly affecting their photophysical and charge separation behavior. As a result of this phenomenon, the electronic excitation is partially localized in one of the molecular branches. However, the intrinsic structural and electronic factors that regulate excited-state symmetry breaking in multibranched systems have hardly been investigated. Herein, we explore these aspects by adopting a joint experimental and theoretical investigation for a class of phenyleneethynylenes, one of the most widely used molecular building blocks for optoelectronic applications. The large Stokes shifts observed for highly symmetric phenyleneethynylenes are explained by the presence of low-lying dark states, as also established by two-photon absorption measurements and TDDFT calculations. In spite of the presence of low-lying dark states, these systems show an intense fluorescence in striking contrast to Kasha''s rule. This intriguing behavior is explained in terms of a novel phenomenon, dubbed “symmetry swapping” that describes the inversion of the energy order of excited states, i.e., the swapping of excited states occurring as a consequence of symmetry breaking. Thus, symmetry swapping explains quite naturally the observation of an intense fluorescence emission in molecular systems whose lowest vertical excited state is a dark state. In short, symmetry swapping is observed in highly symmetric molecules having multiple degenerate or quasi-degenerate excited states that are prone to symmetry breaking.

Highly symmetric multibranched phenyleneethynylenes exhibit intense fluorescence despite the presence of low-lying dark states. The inversion of the energy order of excited states is explained in terms of a novel phenomenon dubbed “symmetry swapping”.     

Native Mass Spectrometry: What is in the Name?

Electrospray ionization mass spectrometry (ESI-MS) is nowadays one of the cornerstones of biomolecular mass spectrometry and proteomics. Advances in sample preparation and mass analyzers have enabled researchers to extract much more information from biological samples than just the molecular weight. In particular, relevant for structural biology, noncovalent protein–protein and protein–ligand complexes can now also be analyzed by MS. For these types of analyses, assemblies need to be retained in their native quaternary state in the gas phase. This initial small niche of biomolecular mass spectrometry, nowadays often referred to as “native MS,” has come to maturation over the last two decades, with dozens of laboratories using it to study mostly protein assemblies, but also DNA and RNA-protein assemblies, with the goal to define structure–function relationships. In this perspective, we describe the origins of and (re)define the term native MS, portraying in detail what we meant by “native MS,” when the term was coined and also describing what it does (according to us) not entail. Additionally, we describe a few examples highlighting what native MS is, showing its successes to date while illustrating the wide scope this technology has in solving complex biological questions.

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Graphical Abstract ?

     

Is the Cassie-Baxter formula relevant?

The utility of the Cassie-Baxter formula to predict the apparent contact angle of a drop on rough hydrophobic surfaces has been questioned recently. To resolve this issue, experimental and numerical data for advancing and receding contact angles are reported. In all cases considered it is seen that contact angles follow the overall trend of the Cassie-Baxter formula, except for the advancing front on pillar type roughness. It is shown that deviations from the Cassie-Baxter angle have a one-to-one correlation with microscopic distortions of the contact line with respect to its configuration in the Cassie-Baxter state.     

Exploring the relationship between cocrystal stability and symmetry: is Wallach's rule applicable to multi-component solids?

Comparison of structure and hydration stability of pairs of chiral and racemic binary cocrystals indicates that the racemic solid is more stable than the chiral one; we illustrate that this difference might arise from intermolecular (crystal packing) factors in one case, while intramolecular (molecular conformation) factors are more significant in the other.     

The σ− selection rule in electron attachment and autoionization of diatomic molecules

It is shown theoretically that Σ⁺ ⇐ Σ⁻ transitions in electron attachment and autionization of diatomic molecules are forbidden. For the verification of this selection rule, two experimental examples are given.     

Chirality: A superselection rule generated by the molecular environment?

The superposition of left- and right-handed forms of a chiral molecule does not exist or is at least very unstable. Frequently, this instability is traced back to the coupling of the molecule to its environment, e.g. the radiation field or collisions with neighbor molecules. The situation is not completely clear, neither theoretically nor experimentally. Here, the theoretical aspects and consequences of the coupling (molecule environment) are discussed.     

Domain-averaged Fermi holes – a new means of visualization of chemical bonds. Bonding in hypervalent molecules

The nature of bonding in several hypervalent molecules was analyzed at the ab initio SCF level using the recently proposed methodology based on the analysis of domain-averaged Fermi holes. The results of the analysis demonstrate that, for sufficiently flexible basis sets, the expansion of the valence shell does indeed take place for second row central atoms in PF₅, SF₄, and SF₆. On the other hand, no such expansion was observed for the first row N atom in NF₅. Received: 1 June 2000 / Accepted: 11 October 2000 / Published online: 23 January 2001     

Adulation or Adulteration? Representing Chemical Dyes in the Victorian Media

This essay describes how the Victorian media reported on the transformation of coal tar into a synthetic palette of colours in the form of aniline and azo dyes. These dyes were the first of many new chemical substances including drugs, perfumes, and flavourings, which chemists began to synthesise and produce on an industrial scale from a waste product of the coal gas industry. Although intended for use in the textile industry, the new dyes soon began to be added to food, becoming one of the first examples of laboratory–created, industrially manufactured chemicals to permeate our daily life in unexpected ways. The essay describes how the initial media portrayal of the dyes as wonders of science became more nuanced as the risks as well as the benefits of the new dyes being used in textiles, and then subsequently in food, became better understood. By examining the media representation of new chemical substances, from their creation in the laboratory to their widespread use in consumer products, sometimes in ways not intended by their creators, my research provides an intriguing case study to add to the growing historiography of how science is represented in the press.     

How are small ions involved in the compaction of DNA molecules?

DNA is a genetic material found in all life on Earth. DNA is composed of four types of nucleotide subunits, and forms a double-helical one-dimensional polyelectrolyte chain. If we focus on the microscopic molecular structure, DNA is a rigid rod-like molecule. On the other hand, with coarse graining, a long-chain DNA exhibits fluctuating behavior over the whole molecule due to thermal fluctuation. Owe to its semiflexible nature, individual giant DNA molecule undergoes a large discrete transition in the higher-order structure. In this folding transition into a compact state, small ions in the solution have a critical effect, since DNA is highly charged. In the present article, we interpret the characteristic features of DNA compaction while paying special attention to the role of small ions, in relation to a variety of single-chain morphologies generated as a result of compaction.     

The Nowotny chimney ladder phases: whence the 14 electron rule?

The late transition metal Nowotny chimney ladder phases (NCLs, T(t)E(m); T, groups 7-9; E, groups 13 and 14) follow a 14 electron rule: the total number of valence electrons per T atom is 14. In this paper, we extract a chemical explanation for this rule from extended Hückel calculations; we focus on RuGa(2), the parent NCL structure. A gap between filled and unfilled bands arises from the occupation of two Ga-Ga bonding/Ru-Ga nonbonding orbitals per RuGa(2), independent of k-point. In addition, the five Ru d levels are filled. Together this makes for 7 filled bands at each k-point, or 14 electrons per Ru. We discuss the connections between this 14 electron rule and the 18 electron rule of organometallic complexes.     

What is the unperturbed state in polymer solutions?

We report theoretical results about amphiphilic random copolymers in a quasi‐ideal conformation with an overall size very close to that of the analogue homopolymers. We found that a few states may coexist with about the same free energy and a similar radius of gyration, but with different intramolecular conformations. We also argue that, in most cases, amphiphilic copolymers may never achieve the unperturbed Θ state, defined thermodynamically by a vanishing second virial coefficient. Thus, we suggest that such copolymers usually show neither an unperturbed conformation nor an unperturbed state from the thermodynamic viewpoint. We also briefly discuss star homopolymers, which show a depression of the Θ temperature with respect to linear chains and a significant, though finite, Θ swelling, as well as linear chains in the Θ state and in the melt. The main general conclusion is that interactions between chain segments do not cancel each other and are non‐negligible. Accordingly, we suggest that the word "unperturbed" be used only with reference to solution thermodynamics and not for the chain size or conformation.     

Fracture of polymer interfaces: what are the relevant length scales?

While it is tempting to relate directly the molecular structure of an interface (between glassy or between semi‐cristalline polymers) with its fracture toughness, these two parameters are simply the two end‐points of a complex network which needs to be understood in order to control the mechanical strength of the interface. The important mechanisms occur at three different length scales: the molecular scale (stress‐transfer across the interface), the microscopic scale (plastic deformation at the crack tip) and the macroscopic scale (loading geometry and elastic constants of the polymers). The couplings existing between these length scales in glassy polymer interfaces are reviewed in this paper in light of the latest experimental studies.     

Mapping fragmental drug-likeness in the MoStBioDat environment: intramolecular hydrogen bonding motifs in β-ketoenols

A detailed knowledge of hydrogen bond geometry and its directional preferences is vital for in silico investigations of the ligand-receptor short-range non-covalent interactions. The spatial arrangement of the carbonyl and hydroxyl groups seems to determine the capability of β-ketoenol derivatives to recognize the surrounding environment by forming inter- and intra-molecular hydrogen bonds (IHB). In the current study we examined the application of the MoStBioDat platform for a massive database screening of the IHB motifs in β-ketoenol subunits (O=C-C=C-OH). Then, the virtual 3D structural data derived from ZINC and PubChem repository were compared to the experimentally determined CSD data. Differences specific for each database were discovered, which indicated inaccuracies in the simulated data.