The Notion of a DNA Minimal Cell: A General Discourse and Some Guidelines for an Experimental Approach

The staggering complexity of even the simplest living microorganisms on Earth elicits the question of whether such complexity is really necessary for life, or whether, instead, the basic functions of cellular life (homeostasis, reproduction, and evolution) can be, in principle, expressed by much simpler unicellular entities that contain only a few dozen genes. This suggests the notion of a minimal cell, i.e., the (potential) cell having the minimal sufficient molecular components to be defined as alive. The conceptual and practical implementation of such minimal cell(s) for our understanding of the notion of life, and also for possible biotechnological applications, is discussed here.     

Synthesis of 1,3-dihydrobenzo[c]furans from ortho-lithiated aryloxiranes

A general method for the synthesis of hydroxyalkyl 1,3-dihydrobenzo[c]furans from ortho-lithiated aryloxiranes and carbonyl compounds is described.     

Papain-induced Oligomerization of α-Amino Acid Esters

Oligomers of leucine, methionine, phenylalanine, and tyrosine were prepared enzymatically (using papain) from the respective methyl esters, with yields ranging from 51–96%. The effect of pH, buffer and salt concentration, and addition of alcohol on the oligomerization of leucine methyl ester was examined. The limits and potentialities of the enzymatic reaction as a method for obtaining monodisperse oligomers are discussed.     

New synthesis of optically active 5-isoxazolidinones and beta-amino acids

A new simple and stereoselective synthesis of 5-isoxazolidinones based on the reaction of lithiated 2-isopropyl-2-oxazolines with nitrones is described. A chiral version of such a methodology allows the preparation of highly enantioenriched 5-isoxazolidinones which are useful precursors for the synthesis of beta-amino acids     

Oxazolinyloxiranyllithium-mediated stereoselective synthesis of alpha-epoxy-beta-amino acids

[reaction: see text] The stereoselective synthesis of novel alpha-epoxy-beta-amino acids is described by a route that combines the chemistry of oxazolinyloxiranyllithiums with that of nitrones. The intermediate trioxadiazadispiro[2.0.4.3]undecanes 4 have been isolated and converted by hydrolysis into epoxy-5-isoxazolidinones 5 which can be transformed into the alpha-epoxy-beta-amino acids 8 by N-O reduction.     

ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature

Background  

We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases.     

An efficient route to tetrahydronaphthols via addition of ortho-lithiated stilbene oxides to alpha,beta-unsaturated fischer carbene Complexes

[reaction: see text] A stereoselective/stereospecific synthesis of polysubstituted tetrahydronaphthols based on the Michael addition of ortho-lithiated stilbene oxides to alpha,beta-unsaturated Fischer carbene complexes followed by an unusual cyclization of the corresponding intermediate in a 6-endo-tet mode is described.     

Stereoselective synthesis of novel 4,5-epoxy-1,2-oxazin-6-ones and alpha,beta-epoxy-gamma-amino acids from beta-lithiated oxazolinyloxiranes and nitrones

[reaction: see text] A stereoselective synthesis of 9,10-epoxy-1,6-dioxa-4,7-diazaspiro[4,5]decanes has been developed on the basis of the addition of beta-lithiated oxazolinyloxiranes to nitrones. Conversion of these spirocyclic derivatives into 4,5-epoxy-1,2-oxazin-6-ones and successively into alpha,beta-epoxy-gamma-amino acids, alpha-hydroxy-gamma-amino acids, and gamma-butyrolactams is described.     

Micellar Solubilization of Biopolymers in Hydrocarbon Solvents III. Empirical Definition of an Acidity Scale in Reverse Micelles

This paper deals with the problem of defining, and measuring, the pH inside the water pool (which we define as pH_wp) of reverse micelles, i.e. micelles formed by surfactants dissolved in apolar solvents in the presence of minimal amounts of water. The conceptual and experimental difficulties are discussed, and it is argued that no absolute determination of pH_wp is possible, mostly because water in the water pools of reverse micelles is a new solvent, for which no standardization of acidity is available. The problem can be approached only on the basis of an empirical acidity scale. An empirical acidity scale for water pools in reverse micelles of bis (2-ethyl-hexyl) sodium sulfosuccinate (AOT) in isooctane has been defined by measuring the ³¹P-chemical shifts of phosphate buffers. The chemical shifts in bulk water were compared to those found in reverse micelles under the assumption that the pK of phosphate ion is the same in the two systems. It was found that in most cases there was little difference (less than 0.4 pH units) between pH_wp and the pH of the starting buffer in bulk water (which we define as pH_st). However, this difference between pH_wp and pH_st may become much larger in certain cases. The difference (pH_wp–pH_st) is measured under a variety of conditions, and this permits the determination of an operational acidity in the micelle water pools as a function of the pH_st with which the aqueous micelles are prepared. The significance of such data for interpreting the behaviour of enzymes confined in the micelles water pool is discussed. Based on the pH_wp scale, the apparent pK_a of phenol-red and 4-nitrophenol were determined in reverse micelles containing different buffers and different water content. The pK_a values obtained were rather sensitive to changes of both these factors, which was taken to signify that organic dies have only a very limited applicability to measure the acidity of the water pools of reverse micelles.     

Emergence in Chemistry: Chemistry as the Embodiment of Emergence

The main aim of the paper is to reinforce the notion that emergence is a basic characteristic of the molecular sciences in general and chemistry in particular. Although this point is well accepted, even in the primary reference on emergence, the keyword emergence is rarely utilized by chemists and molecular biologists and chemistry textbooks for undergraduates. The possible reasons for this situation are discussed. The paper first re-introduces the concept of emergence based on very simple geometrical forms; and considers some simple chemical examples among low and high molecular weight compounds. On the basis of these chemical examples, a few interesting philosophical issues inherent to the field of emergence are discussed – again making the point that such examples, given their clarity and simplicity, permit one to better understand the complex philosophical issues. Thus, the question of predictability is discussed, namely whether and to what extent can emergent properties be predicted on the basis of the component’s properties; or the question of the explicability (a top down process). The relation between reductionism and emergentism is also discussed as well as the notion of downward causality and double causality (macrodeterminism); namely the question whether and to what extent the emergent properties of the higher hierarchic level affect the properties of the lower level components. Finally, the question is analyzed, whether life can be considered as an emergent property. More generally, the final point is made, that the re-introduction of the notion of emergence in chemistry, and in particular in the teaching, may bring about a deeper understanding of the meaning of chemical complexity and may bring chemistry closer to the humanistic areas of philosophy and epistemology. This revised version was published online in July 2006 with corrections to the Cover Date.