Topological stereochemistry

Walba, David M.

doi:10.1016/s0040-4020(01)96671-2

Cited by 408 publications

(224 citation statements)

References 95 publications

Supporting

Mentioning

206

Contrasting

Unclassified

Order By: Relevance

“…[11] At the beginning of the 1980s,o ur group prepared 2,9-diphenyl-1,10-phenanthroline( dpp) for various reasons, mostly in relation to sterically hindering ligands able to favor coordination unsaturation once complexed to rhodium or iridium centers. [6] David spent some time in Strasbourg when he was on sabbatical leave.H ev isited our group and, after several discussions,w ee mbarked on ac ommon project dealing with Cu(dpp) 2 + and related complexes containing two intertwined ligands disposed more or less orthogonally to one another once coordinated to the central Cu I .Atthat time, Cu(dpp) 2 + was unknown, since dpp itself seemed to be anew compound. Thebeginning of this collaboration coincided with another major event, which was the arrival of Christiane Dietrich-Buchecker to our team.…”

Section: Chemical Topologymentioning

confidence: 99%

“…Thebeginning of this collaboration coincided with another major event, which was the arrival of Christiane Dietrich-Buchecker to our team. Christiane had as uperb organic chemistry background and we knew that she had all the necessary expertize for making novel ligands,e ither by herself or associated with the PhD students she would cosupervise with me.C oming back to Cu(dpp) 2 + ,b yl ooking carefully at its three-dimensional representation [8] as shown on Figure 3, it was relatively easy to figure out that this [ 2]rotaxane. The number in square brackets (2 in this case) indicates the number of components incorporated in the interlocking structure.…”

Section: Chemical Topologymentioning

confidence: 99%

“…The number in square brackets (2 in this case) indicates the number of components incorporated in the interlocking structure. A [2]catenane is considered as the prototypeo fmolecules having an onplanar graph. In mathematics, the object consisting of two interlocking rings is called a"Hopf link".…”

Section: Chemical Topologymentioning

confidence: 99%

See 2 more Smart Citations

From Chemical Topology to Molecular Machines (Nobel Lecture)

2017

View full text Add to dashboard Cite

To a large extent, the field of “molecular machines” started after several groups were able to prepare, reasonably easily, interlocking ring compounds (named catenanes for compounds consisting of interlocking rings and rotaxanes for rings threaded by molecular filaments or axes). Important families of molecular machines not belonging to the interlocking world were also designed, prepared, and studied but, for most of them, their elaboration was more recent than that of catenanes or rotaxanes. Since the creation of interlocking ring molecules is so important in relation to the molecular machinery area, we will start with this aspect of our work. The second part will naturally be devoted to the dynamic properties of such systems and to the compounds for which motions can be directed in a controlled manner from the outside, that is, molecular machines. We will restrict our discussion to a very limited number of examples which we consider as particularly representative of the field.

show abstract

Section: Chemical Topologymentioning

confidence: 99%

Section: Chemical Topologymentioning

confidence: 99%

See 1 more Smart Citation

From Chemical Topology to Molecular Machines (Nobel Lecture)

2017

View full text Add to dashboard Cite

show abstract

“…This formulation differs from earlier graph-theoretic treatments of disulfide bonding patterns in that here the direction corresponding to the chemical orientation of the polymeric backbone is included. Earlier approaches used undirected graphs only (Walba, 1985;Mao, 1989).…”

Section: Disulfide Bonding Patterns and Intrinsic Topologiesmentioning

confidence: 99%

Disulfide bonding patterns and protein topologies

Benham

Jafri

1993

Protein Science

View full text Add to dashboard Cite

This paper examines the topological properties of protein disulfide bonding patterns. First, a description of these patterns in terms of partially directed graphs is developed. The topologically distinct disulfide bonding patterns available to a polypeptide chain containing n disulfide bonds are enumerated, and their symmetry and reducibility properties are examined. The theoretical probabilities are calculated that a randomly chosen pattern of n bonds will have any combination of symmetry and reducibility properties, given that all patterns have equal probability of being chosen. Next, the National Biomedical Research Foundation protein sequence and Brookhaven National Laboratories protein structure (PDB) databases are examined, and the occurrences of disulfide bonding patterns in them are determined. The frequencies of symmetric and/or reducible patterns are found to exceed theoretical predictions based on equiprobable pattern selection. Kauzmann's model, in which disulfide bonds form during random encounters as the chain assumes random coil conformations, finds that bonds are more likely to form with near neighbor cysteines than with remote cysteines. The observed frequencies of occurrence of disulfide patterns are found here to be virtually uncorrelated with the predictions of this alternative random bonding model. These results strongly suggest that disulfide bond pattern formation is not the result of random factors, but instead is a directed process.Finally, the PDB structure database is examined to determine the extrinsic topologies of polypeptides containing disulfide bonds. A complete survey of all structures in the database found no instances in which two loops formed by disulfide bonds within the same polypeptide chain are topologically linked. Similarly, no instances are found in which two loops present on different polypeptide chains in a structure are catenated. Further, no examples of topologically knotted loops occur. In contrast, pseudolinking has been found to be a relatively frequent event. These results show a complete avoidance of nontrivial topological entanglements that is unlikely to be the result of chance events. A hypothesis is presented to account for some of these observations. Keywords: covalent bond topology; entanglements; knots; protein structure Topology is the branch of mathematics that studies those properties of shape that remain invariant under continuous deformations. Topological properties naturally subdivide into two types -those that derive from the intrinsic structure of the object under study, and those that relate to how that structure is embedded in space. For example, a closed circle has a different intrinsic topological structure than a finite line segment. One can convert a circle into a line segment only by introducing a cut, which is a discontinuous deformation. As these two structures have different intrinsic topologies, one naturally might expect them also t o have different ranges of possible realizations in space. All embeddings of a finite linear s...

show abstract

“…The rotaxane literature has been extensively reviewed [8][9][10][11][12][13][14][15][16][17][18][19].…”

mentioning

confidence: 99%

Nomenclature for rotaxanes and pseudorotaxanes (IUPAC Recommendations 2008)

Yerin¹,

Wilks²,

Moss

et al. 2008

Pure and Applied Chemistry

View full text Add to dashboard Cite

Republication or reproduction of this report or its storage and/or dissemination by electronic means is Nomenclature for rotaxanes and pseudorotaxanes (IUPAC Recommendations 2008)Abstract: Expanded definitions of rotaxanes and pseudorotaxanes, their components, and other terms concerning rotaxanes are given. The uniform classification and nomenclature principles for naming different types of rotaxanes and pseudorotaxanes are described and illustrated with examples. Recommendations are provided for unambiguous description of rotaxane isomerism with special descriptors that include information about position of rotaxane components.

show abstract

Topological stereochemistry

Cited by 408 publications

References 95 publications

From Chemical Topology to Molecular Machines (Nobel Lecture)

From Chemical Topology to Molecular Machines (Nobel Lecture)

Disulfide bonding patterns and protein topologies

Nomenclature for rotaxanes and pseudorotaxanes (IUPAC Recommendations 2008)

Contact Info

Product

Resources

About