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Tilburg, Netherlands

We have studied with theoretical and mechanistic models the intramolecular 1,2-hydrogen shift in trans-hydroxycarbene-formaldehyde and trans- methylhydroxycarbene-acetaldehyde/vinyl alcohol, and the corresponding intermolecular complexation between hydroxycarbene (cis and trans) with formaldehyde. The purpose of our work is making an analysis of the proposed intramolecular hydrogen shifts mainly based on thermodynamic principles and the product selectivity on monochromatic irradiation of trans-hydroxycarbene in carbon monoxide and molecular hydrogen, and formaldehyde. A geometric visualization of the various intermolecular complexes between hydroxycarbene and formaldehyde, based on ab initio results, is demonstrated and discussed with a concept abstracted from the van't Hoff dynamics for a regular tetrahedron in which the interstitial carbon changes its position from tetrahedral into a trigonal-bipyramidal configuration. This concept has been also used for interactions via proton transfer, concretized as hydrogen-bonded complexation in hydroxycarbene-formaldehyde. With the introduced definitions for various van't Hoff ratio numbers, it was possible to judge the ab initio results of the intermolecular complexes between the hydroxycarbenes and formaldehyde. To make an eye-opener, we discuss the role of the carbene lone pair in hydroxycarbene extended to the formation of mono- and dications demonstrating intermediates or transition states with an exclusive mechanistic behavior. Especially, substituted diaryl methylene dications are of interest for nucleophilic substitution reactions, which occur via an in-plane tetracoordinate carbon intermediate, showing coherence with the orbital organization of methylene dications. A reaction of this type differs fundamentally from the classical S N2 reaction. © 2012 Wiley Periodicals, Inc.

We describe with molecular model studies based on the intrinsic parameters of van't Hoff's regular tetrahedron nucleophilic and electrophilic addition-substitution reactions via a selected reaction coordinate for the displacement of carbon. Geometries of stable, intermediate transition complexes or transition states are compared with the corresponding ab initio values. Specific attention is given on the hypervalent and nonhypervalent character of carbon supported by ab initio calculations, our model consideration and experimental evidence. © 2011 Wiley Periodicals, Inc.

With the van't Hoff model derived from the dynamics of a regular tetrahedron in which the interstitial carbon changes its position from tetrahedral into a trigonal (bi)pyramidal configuration, the introduction of dimensionless ratio numbers (R) can serve to localize significant points on the principal reaction coordinate. These numbers are expressed as R(d) and R(n) based on transition state geometries and the number of electrons involved in the three-center bonding, respectively. Using this concept, we obtain a model for the evaluation of different ab initio calculations based on identity and nonidentity substitution reactions for three-center four- and three-electron bonding transition states. Similar ratio numbers have been derived for proton exchange reactions. The reactions under investigation show clearly that in spite of the differences in chemical outcome the transition steps reduced to the first principles of chemical bonding are similar. Copyright © 2010 Wiley Periodicals, Inc.

We studied various identity nucleophilic substitution reactions based on an SN2 reaction profile. With calculations and experimental geometries concerning the nature of the various complexes indicated as stable, intermediate and transition state we were able to show the additional value of van't Hoff 's tetrahedron by changing its geometry via a trigonal pyramid into a trigonal bipyramid. The ratio of the apical and the corresponding tetrahedral bond distance is then 1.333. This value has been used in general as a calibration point for the understanding of the (in)stabilities of the complex formation on the SN2 reaction coordinate. The relevance of this approach has been also proved for enzymatic reactions focused on carbon and phosphorus substrates. Furthermore, it could be established that identity proton-in-line displacements are fully comparable with the relocation of carbon in a nucleophilic substitution reaction as Cl- + CH3Cl. The significance of this information will afford new insight in the dynamics of a linear three-center four-electron complex. © 2009 Wiley Periodicals.

Buck H.M.,Kasteel Twikkelerf 94
Nucleosides, Nucleotides and Nucleic Acids | Year: 2011

Epigenetic systems involved in the dynamics of gene expression, which are fundamental to cell determination and function without alteration in DNA sequences, are based on methylation of the N-terminal tails of lysine residues and DNA methylation. We demonstrate the vital importance for genetic transfer by different (hydrogen) networks, suggesting a complex interaction between the two epigenetic modifications. In other words, the methylation of local lysines can prescribe C PG methylation, which requires that methylation of histones and DNA are cooperative in carrying out an epigenetic instruction for integrating gene-silencing networks. To give a bio-organic description of the epigenetic coherence between histone and base methylation, we used the well-known B-into Z-DNA dynamics in combination with the unique properties of phosphatemethylated DNA on different levels of chemistry. Copyright © Taylor and Francis Group, LLC.

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