Henry S. Rzepa

The Blue Obelisk-interoperability in chemical informatics.

The Blue Obelisk Movement (http://www.blueobelisk.org/) is the name used by a diverse Internet group promoting reusable chemistry via open source software development, consistent and complimentary chemoinformatics research, open data, and open standards. We outline recent examples of cooperation in the Blue Obelisk group:  a shared dictionary of algorithms and implementations in chemoinformatics algorithms drawing from our various software projects; a shared repository of chemoinformatics data including elemental properties, atomic radii, isotopes, atom typing rules, and so forth; and Web services for the platform-independent use of chemoinformatics programs.

Chemical Markup, XML, and the World Wide Web. 4. CML Schema

A revision to Chemical Markup Language (CML) is presented as a XML Schema compliant form, modularized into nonchemical and chemical components. STMML contains generic concepts for numeric data and scientific units, while CMLCore retains most of the chemical functionality of the original CML 1.0 and extends it by adding handlers for chemical substances, extended bonding models and names. We propose extension via new namespaced components for chemical queries, reactions, spectra, and computational chemistry. The conformance with XML schemas allows much greater control over datatyping, document validation, and structure.

Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles

Chemical markup language (CML) is an application of XML, the extensible markup language, developed for containing chemical information components within documents. Its design supports interoperability with the XML family of tools and protocols. It provides a base functionality for atomic, molecular, and crystallographic information and allows extensibility for other chemical applications. Legacy files can be imported into CML without information loss and can carry any desired chemical ontology. Some applications of CML (Markush structures, chemical searching) will be discussed in later articles. An XML document type declaration (DTD) for CML is included as a Chart.

A Tricyclic Aromatic Isomer of Hexasilabenzene

Aromatic Silicon Benzene has long intrigued chemists on account of the energy stabilization, termed aromaticity, which arises from π-electron delocalization around its ring framework. A persistent question has been how such stabilization would be impacted were the carbons to be replaced by heavier atoms such as silicon. Abersfelder et al. (p. 564) have prepared a benzene analog with Si atoms in place of all six-ring carbons, but a slightly altered bonding framework in which substituents outside the ring are no longer evenly distributed. Instead, the substituents pair up at two Si sites, leaving two other ring sites with no external appendages. The resulting compound no longer has a continuous network of π-electrons, but retains a degree of aromatic stabilization involving sigma and nonbonding electrons. A structural isomer of benzene in which carbon is replaced by silicon exhibits unexpected electronic stabilization. Benzene represents the showcase of Hückel aromaticity. The silicon analog, hexasilabenzene, has consequently been targeted for decades. We now report an intensely green isomer of Si6R6 (R being 2,4,6-triisopropylphenyl) with a tricyclic structure in the solid state featuring silicon atoms with two, one, and no substituents outside the ring framework. The highly dispersed 29Si nuclear magnetic resonance shifts in solution ranging from +125 to −90 parts per million indicate an inhomogeneous electron distribution due to the dismutation of formal oxidation numbers as compared with that of benzene. Theoretical analysis reveals nonetheless the cyclic delocalization of six mobile electrons of the π-, σ- and non-bonding type across the central four-membered ring. For this alternative form of aromaticity, in principle applicable to many Hückel aromatic species, we propose the term dismutational aromaticity.

Some influences of fluorine in bioorganic chemistry

The stereochemical outcome on processing fluorinated substrate analogues by enzymes can often be controlled by electronic and stereoelectronic factors associated with the fluorine atom.

Design, Synthesis, and Evaluation of a Helicenoidal DMAP Lewis Base Catalyst

The design, synthesis, and study of a helical dialkylaminopyridine Lewis base catalyst is reported. Helical DMAP analogue 4 is based upon a helicenoid structure and displays good to excellent levels of selectivity (S ≤ 116) in the kinetic resolution of chiral secondary alcohols. Catalyst 4 displays excellent reactivity with exceptionally low loadings of 0.05 mol % effecting practical levels of selectivity in kinetic resolutions.

The Houk–List transition states for organocatalytic mechanisms revisited

The ten year old Houk–List model for rationalising the origin of stereoselectivity in the organocatalysed intermolecular aldol addition is revisited, using a variety of computational techniques that have been introduced or improved since the original study. Even for such a relatively small system, the role of dispersion interactions is shown to be crucial, along with the use of basis sets where the superposition errors are low. An NCI (non-covalent interactions) analysis of the transition states is able to identify the noncovalent interactions that influence the selectivity of the reaction, confirming the role of the electrostatic NCHδ+⋯Oδ− interactions. Simple visual inspection of the NCI surfaces is shown to be a useful tool for the design of alternative reactants. Alternative mechanisms, such as proton-relays involving a water molecule or the Hajos–Parrish alternative, are shown to be higher in energy and for which computed kinetic isotope effects are incompatible with experiment. The Amsterdam manifesto, which espouses the principle that scientific data should be citable, is followed here by using interactive data tables assembled via calls to the data DOI (digital-object-identifiers) for calculations held on a digital data repository and themselves assigned a DOI.

One Molecule, Two Atoms, Three Views, Four Bonds?

What could be simpler than C2, a well-known diatomic molecule that has the second strongest homonuclear bond (with respect to atomization)? Well, this molecule turns out to be a microcosm of the bonding issues that bother (creatively) chemists, as this trialogue shows. It began when one of the authors published two lively papers on the bonding in C2. A second author became involved when he commented in a blog (a new thing in chemistry) on an isoelectronic molecule. The several studies of the third author, whose favorite molecule this has been for decades, were ignored in those two papers—as you can imagine, at some point he complained. In the spirited conversation that ensued, the authors roam through multiconfigurational states, a quadruple bond between main-group elements, Mulliken s foresight, the utility of VB viewpoints, inorganic structures containing this small organic piece, what makes a diradical, the irrelevance of atomization energies to reactivity and thermodynamic stability, and much more. It s amazing how much heat (and light) can be generated by a simple molecule whose spectrum we ve all seen, yet which you will not hold in a vial.

A Stable Derivative of the Global Minimum on the Si6H6 Potential Energy Surface

The higharomatic stabilization that is conferred by the cyclic delocal-ization of six p electrons distinguishes benzene from itsapproximately 200 theoretically known isomers and accountsfor the ubiquitous occurrence of the benzene motif in manyareas of chemistry. Despite impressive progress regarding thesynthesis of stable compounds with Si Si p bonds,

An x-ray crystallographic, mass spectroscopic, and NMR study of the limonoid insect antifeedant azadirachtin and related derivatives

Abstract The limonoid insect antifeedant azadirachtin (1) may be partially hydrogenated at the C22-C23 position and subsequently treated with an excess of sodium periodate and potassium permanganate in the presence of a base to give detigloyldihydroazadirachtin (4). This compound was examined by X-ray crystallographic techniques which revealed key structural fragments and together with detailed n.m.r. and mass spectroscopic studies allowed the complete unambiguous structure assignment to the parent azadirachtin molecule. Two further compounds, 3-deacetyl-11-desoxyazadirachtin (2), and 3-acetoxy-7-tigloyl-vilasinin lactone (3) were also isolated and characterised from a Senegal sample of neem seed.