Mixis and Diagnôsis: Aristotle and the “Chemistry” of the Sublunary World

In On Generation and Corruption 1.10, Aristotle introduces the new idea of “chemical mixture” (mixis) to explain the constitution of those homogeneous substances from which all things in the sublunary world are comprised. In a mixture, the ingredients interact with one another to give rise to a new substance, qualitatively different, yet preserving the original ingredients in potentia, so that they can be separated again. In Book IV of the Meteorologica, Aristotle further suggests that bodies may be “diagnosed” according to certain passive properties, such as the fusibility of metals. While his theory of mixture has often led historians of science to identify Aristotle as one of the precursors of chemical science, his ideas have also been criticised as archaic, and implicated in a qualitative conception of the cosmos that delayed progress towards quantifying natural phenomena. In this paper, I take up the defence of Aristotle's theory by showing that his concept of mixture is not an obstacle to the development of natural science and chemistry, but, on the contrary, opens the way by offering an advanced model of qualitative analysis which does not exclude the possibility of quantitative development.     

Revisiting the Corey-Chaykovsky reaction: the solvent effect and the formation of β-hydroxy methylthioethers

The classical Corey-Chaykovsky (CC) reaction of ketones in ethereal solvents (i.e., THF or Et₂O) resulted in the production of a significant amount of β-hydroxy methylthioether 2 along with normal epoxide product 1. Some interesting and synthetically useful transformations of the CC reaction product of cyclopropyl ketones were also described.     

Paradigms and paradoxes: decoding the “genetic code”

We propose to keep the term “genetic code” to describe the nucleotide sequence in DNA and RNA and use the term “genetic cipher” to describe the key for decoding the genetic codes of DNA and RNA into the amino acid sequences of proteins.

     

The fast and the slow: folding and trapping of λ6-85

Molecular dynamics simulations combining many microsecond trajectories have recently predicted that a very fast folding protein like lambda repressor fragment λ(6-85) D14A could have a slow millisecond kinetic phase. We investigated this possibility by detecting temperature-jump relaxation to 5 ms. While λ(6-85) D14A has no significant slow phase, two even more stable mutants do. A slow phase of λ(6-85) D14A does appear in mild denaturant. The experimental data and computational modeling together suggest the following hypothesis: λ(6-85) takes only microseconds to reach its native state from an extensively unfolded state, while the latter takes milliseconds to reach compact β-rich traps. λ(6-85) is not only thermodynamically but also kinetically protected from reaching such "intramolecular amyloids" while folding.     

Polymer-supported 1,4-dihydronicotinamide: Synthesis and Application in the Reduction of the Activated Olefins

s: Three new polymer-supported NAD(P)H models (I, II, III) were designed and synthesized, which can efficiently reduce many activated olefins under mild conditions.1 The most advantageous feature of the three NAD(P)H models is (i) easy work-up and separation of the reaction products and (ii) good potential for recycle use of the NAD(P)H models, which makes the three new polymer-supported NAD(P)H models a promising alternative both in research laboratories and in industrial processes.…     

Carbocation-π interaction: the 1,1-dimethylallyl cation and benzene

Computational studies of the interaction of 1,1-dimethylallyl cation with benzene reveal that its potential energy surface has a rich complexity. The lowest energy π-complex, which involves binding of both ends of the cation to the benzene ring, is calculated to be 4.5 kcal mol⁻¹ lower in energy than its related σ-complex. The results provide further support for the idea that π complexation of carbocations is stronger over the periphery of aromatic systems, and offer insight into why biological reactions involving this type of carbocation do not lead via σ-complex formation to electrophilic substitution of the aromatic rings in proteins.     

Metalloid Al- and Ga-clusters: a novel dimension in organometallic chemistry linking the molecular and the solid-state areas?

Formation and fragmentation of metal-metal bonds on the way between stable metal compounds in which the metal atoms are oxidised (e.g. isolated species in solution or metal salts in bulk) and the bulk metal are the fundamental steps to understand this process in which formation and chemical behaviour of metalloid Al and Ga clusters as intermediates are essential. Many examples of metalloid Al and Ga clusters show that their formation reflects a high degree of complexity like that of the simple seeming formation of the bulk metal itself: starting from metastable Al(i) and Ga(i) solutions containing small molecular entities, metalloid clusters grow during many self-organization steps including aggregation as well as irreversible redox cascades. This novel class of clusters seems to open a new dimension in chemistry between the molecular and the solid-state area, because, for the first time, it is shown that under well selected conditions definite molecular species, i.e. metalloid clusters, grow via the formation of additional metal-metal bonds and that the solid metal represents the final step.     

Heisenberg’s chemical legacy: resonance and the chemical bond

Heisenberg’s explanation of how two coupled oscillators exchange energy represented a dramatic success for his new matrix mechanics. As matrix mechanics transmuted into wave mechanics, resulting in what Heisenberg himself described as “…an extraordinary broadening and enrichment of the formalism of the quantum theory”, the term resonance also experienced a corresponding evolution. Heitler and London’s seminal application of wave mechanics to explain the quantum origins of the covalent bond, combined with Pauling’s characterization of the effect, introduced resonance into the chemical lexicon. As the Valence Bond approach gave way to a soon-to-be dominant Molecular Orbital method, our understanding of the term resonance, as it might apply to our understanding the chemical bond, has also changed.     

Computational Toxicology and the Generation of Mechanistic Hypotheses: γ-Butyrolactone

Abstract

In this study, we use SAR approaches in an attempt to elucidate the action of γ-butyrolactone (GBL), an illicit drug and a dietary supplement, that can cause coma and deaths in humans while exhibiting low systemic toxicity towards rodents.

The lack of systemic toxicity of GBL and of its metabolite(s) was also predicted by validated SAR models. In fact using diverse SAR models, the only significant SAR prediction was that GBL had the potential for inhibiting human cytochrome P4502D6 (CYP2D6). However, inhibition of that isozyme is not necessarily associated with toxicity. It is suggested that GBL users also abuse other substances. When GBL inhibits CYP2D6 this may prevent the CYP2D6-mediated detoxification of other toxicants simultaneously consumed by the GBL user.     

Inclusion complexes naphthalene-γ-cyclodextrin-adamantane and naphthalene-γ-cyclodextrin-o-carborane: the structure and luminescence properties

The luminescence properties of inclusion complexes of naphthalene-d₈ with γ-cyclodextrin (γ-CD) in the presence of adamantane or o-carborane added as third parties were studied in aqueous solutions. It was found that the structure of the cage compound added to the aqueous solution of the naphthalene-d₈@γ-CD complex completely determines the luminescence type of the ternary complex. For instance, the intensity of excimer fluorescence (EF) band increases considerably at the expense of reduction of the intensity of monomer fluorescence (MF) band on adding adamantane. On the contrary, adding o-carborane causes a decrease in the intensity of the EF band of naphthalene-d₈ and simultaneous appearance of MF in addition to long-lived room-temperature phosphorescence (RTP) whose lifetime increases from 1.5 s to 9.1 s after deoxygenation of the solution. Structural differences between the complexes affecting their behavior under the action of the third parties were explained using the results of semiempirical quantum chemical calculations.     

Natural and biotech-derived therapeutic proteins: what is the future?

A myriad of novel proteins and ligands of unknown function will be generated by the Human Genomic Project. Due to differences in post-translational processing, proteins produced by recombinant DNA technology may not possess proper biological activity. One way to find their function is to search for their natural counterparts. Proteins are produced in the tissues, and many of them are secreted into plasma and excreted into urine. There is a virtually "unlimited" array of human proteins in our plasma and urine, many of them in a fully active form. They include small molecules like steroids, peptides, and large glycoproteins like human menopausal gonadotropin. A library of plasma and urinary proteins could be developed to serve as a reference for the novel proteins generated by the functional genomic projects.     

Visualisation and integration of G protein-coupled receptor related information help the modelling: Description and applications of the Viseur program

G Protein-Coupled Receptors (GPCRs) constitute a superfamily of receptors that forms an important therapeutic target. The number of known GPCR sequences and related information increases rapidly. For these reasons, we are developing the Viseur program to integrate the available information related to GPCRs. The Viseur program allows one to interactively visualise and/or modify the sequences, transmembrane areas, alignments, models and results of mutagenesis experiments in an integrated environment. This integration increases the ease of modelling GPCRs: visualisation and manipulation improvements enable easier databank interrogation and interpretation. Unique program features include: (i) automatic construction of 'Snake-like' diagrams or hyperlinked GPCR molecular models to HTML or VRML and (ii) automatic access to a mutagenesis data server through the Internet. The novel algorithms or methods involved are presented, followed by the overall complementary features of the program. Finally, we present two applications of the program: (i) an automatic construction of GPCR snake-like diagrams for the GPCRDB WWW server, and (ii) a preparation of the modelling of the 5HT receptor subtypes. The interest of the direct access to mutagenesis results through an alignment and a molecular model are discussed. The Viseur program, which runs on SGI workstations, is freely available and can be used for preparing the modelling of integral membrane proteins or as an alignment editor tool.     

Hairy Core–Shell Nanoparticles via RAFT: Where are the Opportunities and Where are the Problems and Challenges?

The preparation of hairy core–shell nanoparticles including (crosslinked) micelles, unimolecular micelles such as star polymers with block structures in each arm and surface grafted nanoparticles such as inorganic particles via the RAFT process are discussed. The RAFT process is certainly a highly versatile process. However, it should not be forgotten that RAFT polymerization is a process, i.e., superimposed on a conventional free radical process. Furthermore, the livingness of the process is dependent on the accessibility of the RAFT group, which can be hampered in certain approaches such as star synthesis and surface grafting from nanoparticles. Nevertheless, the RAFT process is a versatile toolbox that offers good solutions to a range of problems in the preparation of hairy nanoparticles.

     

Synthesis of the disaccharide CD fragment found in everninomicin-C and -D,avalamycin-A and -C and curamycin-A: stereochemistry at the spiro-ortholactone center

The two isomers at the spiro-ortholactone center of the disaccharide CD fragment of orthosomycins have been synthesized. Their mild acidic hydrolysis was under stereoelectronic control with each isomer leading to only one ester. It is therefore possible, from these results, to deduce the absolute configuration of the spiro-center in natural antibiotics.     

Intra- and inter-monomeric transfers in the light harvesting LHCII complex: the Redfield-Förster picture

We further develop the model of energy transfer in the LHCII trimer based on a quantitative fit of the linear spectra (including absorption (OD), linear dichroism (LD), circular dichroism (CD), and fluorescence (FL)) and transient absorption (TA) kinetics upon 650 nm and 662 nm excitation. The spectral shapes and relaxation/migration rates have been calculated using the combined Redfield-F?rster approach capable of correctly describing fast relaxation within strongly coupled chlorophyll (Chl) a and b clusters and slow migration between them. Within each monomeric subunit of the trimeric complex there is fast (sub-ps) conversion from Chl's b to Chl's a at the stromal side accompanied by slow (>10 ps) equilibration between the stromal- and lumenal-side Chl a clusters in combination with slow (>13 ps) population of Chl's a from the 'bottleneck' Chl a604 site. The connection between monomeric subunits is determined by exciton coupling between the stromal-side Chl's b from the two adjacent subunits (Chl b601'-608-609 cluster) making a simultaneous fast (sub-ps) population of the Chl's a possible from both subunits. Final equilibration occurs via slow (>20 ps) migration between the Chl a clusters located on different monomeric subunits. This migration includes up-hill transfers from the red-most Chl a610-611-612 clusters located at the peripheral side in each subunit to the Chl a602-603 dimers located at the inner side of the trimeric LHCII complex.     

Sol–Gel Derived Organic and Inorganic Hybrid Materials for Photonic Applications: Contribution to the Correlation Between the Material Structure and the Transmission in the Near Infrared Region

A promising way of fabricating integrated optics components is based on the sol–gel synthesis and photocuring of organic-inorganic hybrid materials. However, the main factor limiting the development of passive devices is the propagation losses. Moreover, the possibility to compensate these attenuations by optical amplification is competed with the multiphonon relaxation associated to the presence of OH groups. To our knowledge, OH groups were always shown as the main responsible for attenuation at the telecommunication wavelengths, namely at 1310 and 1550 nm, although the matrix is composed of organic species which can contribute to absorptions in this spectral range. This paper deals with spectroscopic and optical characterizations of a well established organic and inorganic hybrid material in order to determine the contribution of each molecular groups to the attenuation at the aforementioned wavelengths.     

Experimental and theoretical study of N-hexylcytosine and N-hexylcytosinium nitrate: the crucial role of hydrophobic and anion–π interactions

We report the synthesis and X-ray characterization of N¹-hexylcytosine (1) and N¹-hexylcytosinium nitrate (2). N¹-hexylcytosine (1) does not follow the same behaviour previously described for N¹-hexylthymine and N¹-hexyluracil in the solid state. This different behavior has been analyzed by means of density functional theory (DFT) calculations including the latest available correction for dispersion (D3). In addition hydrophobic and anion–π noncovalent interactions play a key role in stabilizing the 3D architectures of the compounds, which have been energetically studied using theoretical calculations and compared with similar structures retrieved from the Cambridge Structural Database (CSD). The anion–π–anion binding mode observed for nitrate in compound 2 is also observed in several crystal structures involving cytosine ring coordinated to transition metals.     

Thermally Stable and Organo-soluble Polyamides Containing Triazine Rings and Ether Linkages in the Main Chain: Synthesis and Characterization

In order to synthesize new polyamide(PA) 5 and copolyamides(Co PA) 7a-7d, a new-type of dicarboxylic acid containing triazine ring was successfully synthesized from 2,4-dichloro-6-methoxy-s-triazine 1 and 4-aminobenzoic acid. New polyamide 5 containing triazine moiety was prepared from 4,4'-(6-methoxy-1,3,5-triazine-2,4-diyl)bis(azanediyl)dibenzoic acid 3 and 4,4′-diaminodiphenylether by direct polycondensation reaction. Then new series thermally stable copolyamides 7a-7d with high solubility in common organic solvents were synthesized from the direct polycondensation reaction of diacid 3 as a first monomer, aliphatic-aromatic diacids 6a-6d as second diacids and 4,4′-diaminodiphenylether. All of the above polymers were fully characterized by 1H-NMR and FTIR spectroscopy, elemental analysis(CHN), inherent viscosity, solubility tests, gel permeation chromatography(GPC), differential scanning calorimetry(DSC) and thermogravimetric analysis(TGA). The resulted Co PAs 7a-7d have shown good inherent viscosities, solubility and thermal properties.