Halogen bonding: the σ-hole

Halogen bonding refers to the non-covalent interactions of halogen atoms X in some molecules, RX, with negative sites on others. It can be explained by the presence of a region of positive electrostatic potential, the σ-hole, on the outermost portion of the halogen’s surface, centered on the R–X axis. We have carried out a natural bond order B3LYP analysis of the molecules CF₃X, with X = F, Cl, Br and I. It shows that the Cl, Br and I atoms in these molecules closely approximate the configuration, where the z-axis is along the R–X bond. The three unshared pairs of electrons produce a belt of negative electrostatic potential around the central part of X, leaving the outermost region positive, the σ-hole. This is not found in the case of fluorine, for which the combination of its high electronegativity plus significant sp-hybridization causes an influx of electronic charge that neutralizes the σ-hole. These factors become progressively less important in proceeding to Cl, Br and I, and their effects are also counteracted by the presence of electron-withdrawing substituents in the remainder of the molecule. Thus a σ-hole is observed for the Cl in CF₃Cl, but not in CH₃Cl. Figure Schematic representation of the atomic charge generation. The molecular electrostatic potential (MEP) is calculated using the AM1* Hamiltonian. The semiempirical MEP is then scaled to DFT or ab initio level and atomic charges are generated from it by the restrained electrostatic potential (RESP) fit method.     

ETS-NOCV description of σ-hole bonding

The ETS-NOCV analysis was applied to describe the σ-hole in a systematic way in a series of halogen compounds, CF₃-X (X?=?I, Br, Cl, F), CH₃I, and C(CH3)_nH_3-n-I (n?=?1,2,3), as well as for the example germanium-based systems. GeXH₃, X?=?F, Cl, H. Further, the ETS-NOCV analysis was used to characterize bonding with ammonia for these systems. The results show that the dominating contribution to the deformation density, Δρ ₁ , exhibits the negative-value area with a minimum, corresponding to σ-hole. The “size” (spatial extension of negative value) and “depth” (minium value) of the σ-hole varies for different X in CF₃-X, and is influenced by the carbon substituents (fluorine atoms, hydrogen atoms, methyl groups). The size and depth of σ-hole decreases in the order: I, Br, Cl, F in CF₃-X. In CH₃-I and C(CH3)_nH_3-n-I, compared to CF₃-I, introduction of hydrogen atoms and their subsequent replacements by methyl groups lead to the systematic decrease in the σ-hole size and depth. The ETS-NOCV σ-hole picture is consistent with the existence the positive MEP area at the extension of σ-hole generating bond. Finally, the NOCV deformation density contours as well as by the ETS orbital-interaction energy indicate that the σ-hole-based bond with ammonia contains a degree of covalent contribution. In all analyzed systems, it was found that the electrostatic energy is approximately two times larger than the orbital-interaction term, confirming the indisputable role of the electrostatic stabilization in halogen bonding and σ-hole bonding.

Discovery of σ-hole interactions involving ylides

The positive electrostatic potentials (σ-hole) have been found in ylides CH₂XH₃ (X = P, As, Sb) and CH₂YH₂ (Y = S, Se, Te), on the outer surfaces of group VA and VIA atoms, approximately along the extensions of the C–X and C–Y bonds, respectively. These electrostatic potentials suggest that the above ylides can interact with nucleophiles to form weak, directional noncovalent interactions similar to halogen bonding interactions. MP2 calculations have confirmed the formation of CH₂XH₃···HM complexes (X = P, As, Sb; M = BeH, ZnH, MgH, Li, Na). The interaction energies, interaction distances, topological properties (electron density and its Laplacian), and energy properties (kinetic electron energy density and potential electron energy density) at the X(1)···H(10) bond critical points are all correlated with the most negative electrostatic potential value of HM, indicating that electrostatic interactions play an important role in these weak X···H interactions. Similar to the halogen bonding interactions, weak interactions involving ylides may be significant in several areas such as organic synthesis, crystal engineering, and design of new materials.     

The protonated 2-halogenated imidazolium cation as the noncovalent interaction donor: the σ-hole and π-hole interactions

The σ-hole and π-hole of the protonated 2-halogenated imidazolium cation (XC₃H₄N₂ ⁺; X = F, Cl, Br, I) were investigated and analyzed. The monomers of (CH₃)₃SiY(Y=F, Cl, Br, I), considered as the Lewis base, were combined with the σ-hole and π-hole of XC₃H₄N₂ ⁺ to form the σ-hole and π-hole interactions in the bimolecular complexes (CH₃)₃SiY?·?·?·?XC₃H₄N₂ ⁺ and (CH₃)₃SiY?·?·?·?C₃(X)H₄N₂ ⁺(X/Y=F, Cl, Br, I), respectively. For both the σ-hole and π-hole interactions, the equilibrium geometries of complexes show regular changes according to the sequence of heavy sequence of the noncovalent interaction acceptors and donors. The electrostatic energy is the main contribution in the formation of both kinds of interactions, it has linear relations with the V _S,max values of σ-hole and the V′ _S,max values of π-hole. Both the σ-hole and π-hole interactions belong to the closed-shell and noncovalent interactions. The π-hole interactions are stronger than the σ-hole interactions. For the π-hole interactions, the contribution percents of the dispersion energies are somewhat greater than those of the σ-hole interactions, while it is contrary for the polarization energy.

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Graphical Abstract The protonated 2-halogenated imidazolium cation as the noncovalent interaction donor: the σ-hole and π-hole interactions?

     

Enhancing effects of hydrogen/halogen bonds on σ-hole interactions involving ylide

PqsD mediates the conversion of anthraniloyl-coenzyme A (ACoA) to 2-heptyl-4-hydroxyquinoline (HHQ), a precursor of the Pseudomonas quinolone signal (PQS) molecule. Due to the role of the quinolone signaling pathway of Pseudomonas aeruginosa in the expression of several virulence factors and biofilm formation, PqsD is a potential target for controlling this nosocomial pathogen, which exhibits a low susceptibility to standard antibiotics. PqsD belongs to the β-ketoacyl-ACP synthase family and is similar in structure to homologous FabH enzymes in E. coli and Mycobacterium tuberculosis. Here, we used molecular dynamics simulations to obtain the structural position of the substrate ACoA in the binding pocket of PqsD, and semiempirical molecular orbital calculations to study the reaction mechanism for the catalytic cleavage of ACoA. Our findings suggest a nucleophilic attack of the deprotonated sulfur of Cys112 at the carbonyl carbon of ACoA and a switch in the protonation pattern of His257 whereby N_δ is protonated and the proton of N_ε is shifted to the sulfur of CoA during the reaction. This is in agreement with the experimentally determined decreased catalytic activity of the Cys112Ser mutant, whereas the Cys112Ala, His257Phe, and Asn287Ala mutants are all inactive. ESI mass-spectrometric measurements of the Asn287Ala mutant show that anthraniloyl remains covalently bound to Cys112, thus further supporting the inference from our computed mechanism that Asn287 does not take part in the cleavage of ACoA. Since this mutant is inactive, we suggest instead that Asn287 must play an essential role in the subsequent formation of HHQ in vitro.     

Explosive Expansion of βγ-Crystallin Genes in the Ancestral Vertebrate

In jawed vertebrates, βγ-crystallins are restricted to the eye lens and thus excellent markers of lens evolution. These βγ-crystallins are four Greek key motifs/two domain proteins, whereas the urochordate βγ-crystallin has a single domain. To trace the origin of the vertebrate βγ-crystallin genes, we searched for homologues in the genomes of a jawless vertebrate (lamprey) and of a cephalochordate (lancelet). The lamprey genome contains orthologs of the gnathostome βB1-, βA2- and γN-crystallin genes and a single domain γN-crystallin-like gene. It contains at least two γ-crystallin genes, but lacks the gnathostome γS-crystallin gene. The genome also encodes a non-lenticular protein containing βγ-crystallin motifs, AIM1, also found in gnathostomes but not detectable in the uro- or cephalochordate genome. The four cephalochordate βγ-crystallin genes found encode two-domain proteins. Unlike the vertebrate βγ-crystallins but like the urochordate βγ-crystallin, three of the predicted proteins contain calcium-binding sites. In the cephalochordate βγ-crystallin genes, the introns are located within motif-encoding region, while in the urochordate and in the vertebrate βγ-crystallin genes the introns are between motif- and/or domain encoding regions. Coincident with the evolution of the vertebrate lens an ancestral urochordate type βγ-crystallin gene rapidly expanded and diverged in the ancestral vertebrate before the cyclostomes/gnathostomes split. The β- and γN-crystallin genes were maintained in subsequent evolution, and, given the selection pressure imposed by accurate vision, must be essential for lens function. The γ-crystallin genes show lineage specific expansion and contraction, presumably in adaptation to the demands on vision resulting from (changes in) lifestyle.     

Argonaute2 Mediates Compensatory Expansion of the Pancreatic β Cell

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Analysis of the molecular interactions of the potent analgesic S1RA with the σ1 receptor

The highly selective σ₁ receptor antagonist S1RA is endowed with a surprisingly high affinity for its target protein given a missing fundamental hydrophobic pharmacophoric requirement. Here we show that, with respect to other potent σ₁ ligands, S1RA is able to compensate this loss by fulfilling all other pharmacophoric requirements and by gaining in solvation energy     

The history of the homology concept and the “Phylogenetisches Symposium”

The homology concept has had a long and varied history, starting out as a geometrical term in ancient Greece. Here we describe briefly how a typological use of homology to designate organs and body parts in the same position anatomically in different organisms was changed by Darwin’s theory of evolution into a phylogenetic concept. We try to indicate the diversity of opinions on how to define and test for homology that has prevailed historically, before the important books by Hennig (1950. Grundzüge einer Theorie der Phylogenetischen Systematik. Deutscher Zentralverlag, Berlin) and Remane (1952. Die Grundlagen des Natürlichen Systems, der Vergleichenden Anatomie und der Phylogenetik. Geest & Portig, Leipzig) brought more rigor into both the debate on homology and into the usage of the term homology among systematists. Homology as a theme has recurred repeatedly throughout the history of the “Phylogenetisches Symposium” and we give a very brief overview of the different aspects of homology that have been discussed at specific symposia over the last 48 years. We also honour the fact that the 2004 symposium was held in Jena by pointing to the roles played by biologists active in Jena, such as Ernst Haeckel and Carl Gegenbaur, in starting the development towards a homology concept concordant with an evolutionary world view. As historians of biology, we emphasize the importance of major treatises on homology and its history that may be little read by systematists active today, and have sometimes also received less attention by historians of biology than they deserve. Prominent among these are the works of Dietrich Starck, who also happened to be both a student, and later a benefactor, of systematics at Jena University.     

For debate: Starling's curve of the pancreas--overuse of a concept?

It is commonly accepted that insulin secretion follows the pattern of an inverted U, also termed 'Starling's curve of the pancreas' during the natural history of hyperglycemia in glucose intolerance and type 2 diabetes. This concept is based on the cross-sectional observation that insulin concentrations initially increase when insulin sensitivity declines (as a consequence of obesity, for example) and decrease when glucose tolerance deteriorates (impaired glucose tolerance or overt type 2 diabetes). The initial increase in insulin concentrations has been viewed as 'hypersecretion' of insulin, thought to indicate that beta cell dysfunction is not etiological but secondary in nature. However, this view is oblivious to the now well-established fact that assessment of insulin secretion must account for individual insulin sensitivity. Here, we revisit the concept of Starling's curve of the pancreas based on first-phase C-peptide concentrations (hyperglycemic clamp) from subjects with normal glucose tolerance (n=66), impaired glucose tolerance (n=19) and mild type 2 diabetes (n=9). In absolute terms, first-phase C-peptide concentrations plotted against increasing fasting glucose concentrations indeed followed an inverted U. However, adjusted for direct and indirect measures of insulin sensitivity (insulin sensitivity index from the hyperglycemic clamp, body mass index, age and sex), first-phase C-peptide concentrations of the same individuals tended to decrease steadily. In conclusion, while the Starling curve exists for insulin concentrations, and perhaps also for insulin secretion, it does not hold for beta-cell function if that term were to imply appropriateness of insulin secretion (based on a formal test of glucose-stimulated insulin secretion) for the degree of insulin resistance, as it should.     

Exploring the concept of interaction computing through the discrete algebraic analysis of the Belousov–Zhabotinsky reaction

Interaction computing (IC) aims to map the properties of integrable low-dimensional non-linear dynamical systems to the discrete domain of finite-state automata in an attempt to reproduce in software the self-organizing and dynamically stable properties of sub-cellular biochemical systems. As the work reported in this paper is still at the early stages of theory development it focuses on the analysis of a particularly simple chemical oscillator, the Belousov–Zhabotinsky (BZ) reaction. After retracing the rationale for IC developed over the past several years from the physical, biological, mathematical, and computer science points of view, the paper presents an elementary discussion of the Krohn–Rhodes decomposition of finite-state automata, including the holonomy decomposition of a simple automaton, and of its interpretation as an abstract positional number system. The method is then applied to the analysis of the algebraic properties of discrete finite-state automata derived from a simplified Petri net model of the BZ reaction. In the simplest possible and symmetrical case the corresponding automaton is, not surprisingly, found to contain exclusively cyclic groups. In a second, asymmetrical case, the decomposition is much more complex and includes five different simple non-abelian groups whose potential relevance arises from their ability to encode functionally complete algebras. The possible computational relevance of these findings is discussed and possible conclusions are drawn.     

Myogenesis of Malacostraca – the “egg-nauplius” concept revisited

Background

Malacostracan evolutionary history has seen multiple transformations of ontogenetic mode. For example direct development in connection with extensive brood care and development involving planktotrophic nauplius larvae, as well as intermediate forms are found throughout this taxon. This makes the Malacostraca a promising group for study of evolutionary morphological diversification and the role of heterochrony therein. One candidate heterochronic phenomenon is represented by the concept of the ‘egg-nauplius’, in which the nauplius larva, considered plesiomorphic to all Crustacea, is recapitulated as an embryonic stage.

Results

Here we present a comparative investigation of embryonic muscle differentiation in four representatives of Malacostraca: Gonodactylaceus falcatus (Stomatopoda), Neocaridina heteropoda (Decapoda), Neomysis integer (Mysida) and Parhyale hawaiensis (Amphipoda). We describe the patterns of muscle precursors in different embryonic stages to reconstruct the sequence of muscle development, until hatching of the larva or juvenile. Comparison of the developmental sequences between species reveals extensive heterochronic and heteromorphic variation. Clear anticipation of muscle differentiation in the nauplius segments, but also early formation of longitudinal trunk musculature independently of the teloblastic proliferation zone, are found to be characteristic to stomatopods and decapods, all of which share an egg-nauplius stage.

Conclusions

Our study provides a strong indication that the concept of nauplius recapitulation in Malacostraca is incomplete, because sequences of muscle tissue differentiation deviate from the chronological patterns observed in the ectoderm, on which the egg-nauplius is based. However, comparison of myogenic sequences between taxa supports the hypothesis of a zoea-like larva that was present in the last common ancestor of Eumalacostraca (Malacostraca without Leptostraca). We argue that much of the developmental sequences of larva muscle patterning were retained in the eumalacostracan lineage despite the reduction of free swimming nauplius larvae, but was severely reduced in the peracaridean clade.

     

Effect of structural modification in the amine portion of substituted aminobutyl-benzamides as ligands for binding σ1 and σ2 receptors

5-Bromo-N-[4-(6,7-dimethoxy-3,4-dihydro-1H-isoquinolin-2-yl)-butyl)]-2,3-dimethoxy-benzamide (1) is one of the most potent and selective σ(2) receptor ligands reported to date. A series of new analogs, where the amine ring fused to the aromatic ring was varied in size (5-7) and the location of the nitrogen in this ring was modified, has been synthesized and assessed for their σ(1)/σ(2) binding affinity and selectivity. The binding affinity of an open-chained variant of 1 was also evaluated. Only the five-membered ring congener of 1 displayed a higher σ(1)/σ(2) selectivity, derived from a higher σ(2) affinity and a lower σ(1) affinity. Positioning the nitrogen adjacent to the aromatic ring in the five-membered and six-membered ring congeners dramatically decreased affinity for both subtypes. Thus, location of the nitrogen within a constrained ring is confirmed to be key to the exceptional σ(2) receptor binding affinity and selectivity for this active series.     

A critical review of the ‘neugliederung’ concept in relation to the development of the vertebral column

Summary The literature on the early embryonic development of the vertebral column in various animal species was analyzed to evaluate so many unrelated or contradictory observations. The recurring problems are described. One of the first was the lack of correspondence between the metameric boundaries of the primitive vertebral bodies arising from the somites and those of the adult vertebral bodies, as presumably shown by their relationship to the vertebral processes and spinal nerves. A century ago, Remak introduced the concept of Neugliederung, according to which the ultimate vertebral body boundaries are determined by a shift of a half segment in comparison with the earlier segment boundaries.     

Analysis of the expression and function of the σB-dependent general stress regulon of Bacillus subtilis during slow growth

Glucose-limited continuous cultures were used to analyze σ^B activity at decreasing growth rates. Expression of the σ^B-dependent genes gsiB and ctc started to increase at a growth rate of 0.2 h^–1, and both genes were induced approximately fivefold at a growth rate of 0.1 h^–1 as compared to expression at the maximal growth rate. However, maximal σ^B activity was only reached when the growth stopped as a result of the exhaustion of the carbon and energy source glucose. During glucose-limited growth, increased expression of the general stress regulon at growth rates below 0.2 h^–1 did not provide wild-type cells with a growth advantage over sigB mutants. Instead, expression of the stress regulon seems to constitute a significant burden during glucose-limited growth, resulting in a selective growth advantage of the sigB mutant as compared to the wild-type at a growth rate of 0.08 h^–1. Received: 7 January 1999 / Accepted: 22 March 1999