Hydrocarbon links in an octet truss

We use the octet truss of R. Buckminster Fuller to develop a geometric placement method for synthesizing braid representations of knots and links of oligo (phenylene ethynylene)s using the 60° ortho, 120° meta or 180° para phenyl ring substitution angles and respecting the van der Waals repulsion constraints. We show that any knot or link can be realized by a phenylene ethynylene oligomer modeled on the octet truss. Use of this lattice is motivated by the structural constraints of these phenylene ethynylene units. Where in bio-organic chemistry, questions often involve identifying existing knots, for example in DNA strands, organic synthesis is concerned with assembling molecular structures that can be verified to exist in a desired knot topology. This physical realization of a knot as a construction of common organic molecular subunits then facilitates further study of the properties of knotted molecules in general.     

Simulations of the untying of molecular friction knots between individual polymer strands

The dynamics of molecular knots is implicated in a broad range of phenomena, from DNA replication to relaxation of polymer melts. Motivated by the recent experiments, in which biopolymer knots have been observed and manipulated at a single-molecule level, we have used computer simulations to study the dynamics of "friction knots" joining individual polymer strands. A friction knot splicing two ropes becomes jammed when the ropes are pulled apart. In contrast, molecular friction knots eventually become undone by thermal motion. We show that depending on the knot type and on the polymer structure, a microscopic friction knot can be strong (the time tau the knot stays tied increases with the force F applied to separate the strands) or weak (tau decreases with increasing F). The strong knot behavior is a microscopic analog of macroscopic knot jamming. We further describe a simple model explaining these behaviors.     

Knotting and threading of molecules: chemistry and chirality of molecular knots and their assemblies

How and why do molecules tangle or thread? Investigations of molecular knots (knotanes) may shed some light on the mechanisms of (supra)molecular templation and the folding of molecules that result in intertwining. The topological chirality of these fascinating molecules leads to new types of isomerism and paves the way to nanosized molecular motors. Their preparation and derivatization makes high demands on modern synthetic methods and analytical separation since molecular knots are formed in a more or less planned design based on metal coordination or hydrogen‐bonding patterns. This Review describes the development of templation techniques for the synthesis of knotanes and their chiral resolution as well as their selective functionalization and use as building blocks in the synthesis of higher knotane assemblies. Such assemblies can possess linear, branched, or even macrocyclic structures which, on the one hand, introduce unprecedented isomeric compositions that arise from multiple topological stereogenic units and, on the other, define new types of artificial macromolecules beyond polymers and dendritic species.     

Oligothiophene catenanes and knots: a theoretical study

Oligothiophene [2]catenanes and knots containing up to 28 thiophene units have been studied at the BHandHLYP/3-21G level of theory. Small knots (less than 22 thiophene units) and [2]catenanes (less than 18 thiophene units) are strained molecules. Larger knots and [2]catenanes are almost strain-free. [2]Catenanes and knots having less than 18 and 24 units, respectively, show transversal electronic coupling destroying one-dimensionality of molecules reflecting in smaller band gaps compared to larger knots and catenanes. Ionization potentials of knots and catenanes are always higher compared to that of lineal oligomers due to less effective conjugation. Polaron formation in catenanes is delocalized only over one ring, leaving another intact. In the case of a knot containing 22 thiophene units, estimated polaron delocalization is 8 to 9 repeating units.     

Reaction of N-alkylglycolurils with electrophilic reagents

The N-hydroxymethylation, N-acetylation, and N-acetoxymethylation of mono-, di-, and trialkylglycolurils by reaction with the electrophilic reagents formaldehyde and acetaldehyde have been studied. General methods have been developed for the preparation of mono-, di-, and tri-N-hydroxymethylglycolurils by treatment of differently substituted N-alkylglycolurils with formaldehyde (as hemiformal in methanol) and the synthesis of di-N-and tri-N-acetyl-or N-acetoxymethylglycolurils via the electrophilic substitution of hydrogen atoms for an acetyl group at the nitrogen or oxygen atoms in the hydroxymethyl groups of glycolurils using acetic anhydride. The regioselectivity of the reaction of the 2-t-Bu-and 2-c-C₆H₁₁-glycolurils with formaldehyde has been shown to yield a 4,6-di(hydroxymethyl) derivative. It was found that the hydroxymethylation of 2,4-and 2,6-dialkylglycolurils occurs regioselectively with a stoichiometric ratio of glycoluril to hemiformal and permits preparation of their mono-and dihydroxymethyl derivatives. The enantiomeric analysis of the obtained compounds has been carried out for the first time using HPLC on chiral phases. X-ray analysis has been carried out on the previously unreported racemic 2,6-diacetoxymethyl-4,8-dimethylglycoluril. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 411–423, March, 2006.     

The electron-impact-induced fragmentation of some methylated histamines

The mass spectra of twelve mono-, di- and tri-methyl substituted histamines are reported and discussed. It is shown that the position(s) of substitution may be deduced from a study of the fragmentation pattern, relative intensity and metastable ions allowing unambiguous identification of structure.     

Synthesis of Tetraazide Derivatives of <Emphasis Type="Italic">p-tert</Emphasis>-Butylcalix[4]arene Using Copper-Catalyzed Nucleophilic Aromatic Substitution

Aromatic azido derivatives of p-tert-butylcalix[4]arene have been obtained for the first time using copper-catalyzed nucleophilic aromatic substitution of azide anion for bromide in 5,11,17,23-tetrabromo- 25,26,27,28-tetrabuthoxycalix[4]arene in a dioxane–water (3: 1) solvent mixture with N,N-dimethylethylenediamine as a stabilizing ligand for copper(I). When the reaction is carried out under with microwave heating, partial substitution products (mono-, distally di-, proximally di-, and trisubstituted) can be isolated in satisfactory yields.     

Study of the electrophilic substitution of alkyl-, aryl-, and aralkyl-5(6)-hydroxybenzimidazoles

A series of new 4-sulfo-5(6)-hydroxybenzimidazoles was obtained including mono-, di-, and trinitro derivatives of 2-phenyl- and 2-benzyl-5-hydroxybenzimidazoles. Aromatic groups at C², in contrast to alkyl groups, enhance the reactivity of the benzimidazole system in electrophilic substitution.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 8, pp. 1888–1892, August, 1990.     

Binaphthalene molecules with tetrathiafulvalene units: CD spectrum modulation and new chiral molecular switches by reversible oxidation and reduction of tetrathiafulvalene units

By combining the features of binaphthalene and tetrathiafulvalene (TTF), compounds 1-4 were designed for studies of chiral molecular switches. Absorption and CD spectral studies clearly indicate that the CD spectra resulting from axial chiral binaphthalene units can be modulated through the redox reactions of TTF units, which means new chiral molecular switches can be established on the basis of binaphthalene molecules with TTF units. The reference compound 5, which has one TTF unit rather than two as in the case of compounds 1, 3, and 4, failed to show such property, hinting that the presence of two or more TTF units is required for the realization of CD spectrum modulation. In addition, the manner of the CD spectrum modulation has been found to be dependent on the way TTF units are linked to the binaphthalene skeleton, in terms of the linker length, the positions for substitution, and the number of TTF units.     

Dynamic chirality, chirality transfer and aggregation behaviour of dithienylethene switches

The synthesis and characterisation of a series of chiral and achiral low molecular weight organogelators (LMWGs) based on bis-amide substituted dithienylethene photochromic switches is reported. The LMWGs gelate a range of solvents depending on the specific functionalisation of the hydrogen bonding amide groups. In mixtures of chiral and achiral LMWGs the stereochemical outcome of the chiral aggregation is determined by the chiral LMWG molecules in most cases. However, for the first time we demonstrate that the stereochemical outcome of the aggregation can be influenced by the achiral LWMG molecules in some cases. Furthermore specific π-π (and/or van der Waals) interactions of chiral LMWGs 1-3o with the solvent allow the solvent to influence the control of chirality of aggregation. This influence of the solvent has a dramatic effect on whether four- or two-gel states are available.     

Distinctive features and challenges in catenane chemistry

From being an aesthetic molecular object to a building block for the construction of molecular machines, catenanes and related mechanically interlocked molecules (MIMs) continue to attract immense interest in many research areas. Catenane chemistry is closely tied to that of rotaxanes and knots, and involves concepts like mechanical bonds, chemical topology and co-conformation that are unique to these molecules. Yet, because of their different topological structures and mechanical bond properties, there are some fundamental differences between the chemistry of catenanes and that of rotaxanes and knots although the boundary is sometimes blurred. Clearly distinguishing these differences, in aspects of bonding, structure, synthesis and properties, between catenanes and other MIMs is therefore of fundamental importance to understand their chemistry and explore the new opportunities from mechanical bonds.

Catenane chemistry is closely associated with that of rotaxane and knot, and this perspective highlights their similarities and differences in various aspects including synthesis, structure and properties.     

Effects of turn-structure on folding and entanglement in artificial molecular overhand knots

The length and constitution of spacers linking three 2,6-pyridinedicarboxamide units in a molecular strand influence the tightness of the resulting overhand (open-trefoil) knot that the strand folds into in the presence of lanthanide(iii) ions. The use of β-hairpin forming motifs as linkers enables a metal-coordinated pseudopeptide with a knotted tertiary structure to be generated. The resulting pseudopeptide knot has one of the highest backbone-to-crossing ratios (BCR)—a measure of knot tightness (a high value corresponding to looseness)—for a synthetic molecular knot to date. Preorganization in the crossing-free turn section of the knot affects aromatic stacking interactions close to the crossing region. The metal-coordinated pseudopeptide knot is compared to overhand knots with other linkers of varying tightness and turn preorganization, and the entangled architectures characterized by NMR spectroscopy, ESI-MS, CD spectroscopy and, in one case, X-ray crystallography. The results show how it is possible to program specific conformational properties into different key regions of synthetic molecular knots, opening the way to systems where knotting can be systematically incorporated into peptide-like chains through design.

Spacers linking 2,6-pyridinedicarboxamide units influence the tightness of the corresponding lanthanide-coordinated overhand knot. β-Hairpin forming motifs generate a metal-coordinated pseudopeptide with a knotted tertiary structure.     

Alkene-directed, nickel-catalyzed alkyne coupling reactions

In alkene-directed, nickel-catalyzed coupling reactions of 1,3-enynes with aldehydes and epoxides, the conjugated alkene dramatically enhances reactivity and uniformly directs regioselectivity, independent of the nature of the other alkyne substituent (aryl, alkyl (1 degrees , 2 degrees , 3 degrees )) or the degree of alkene substitution (mono-, di-, tri-, and tetrasubstituted). These observations are best explained by a temporary interaction between the alkene and the transition metal center during the regioselectivity-determining step. The highly substituted 1,3-diene products are useful in organic synthesis and, in conjunction with a Rh-catalyzed, site-selective hydrogenation, afford allylic and homoallylic alcohols that previously could not be prepared in high regioselectivity (or at all) with related Ni-catalyzed alkyne coupling reactions.     

Novel chiral "calixsalen" macrocycle and chiral robson-type macrocyclic complexes

A family of novel chiral "calixsalen" Schiff base macrocycles R,R-H(3)L4, R,R-H(3)L5, containing three chiral diamino moieties were synthesized by an efficient self-assembly and characterized by (1)H and (13)C NMR, mass spectrometry, and X-ray diffraction. The systematic synthesis, structure, and coordination properties of the [2 + 2] and [3 + 3] Robson-type Schiff base macrocyclic mono-, di-, tri-, and tetranuclear metal complexes were explored.     

Di-(R,R)-1-[10-(1-hydroxy-2,2,2-trifluoroethyl)-9-anthryl]-2,2,2-trifluoroethyl muconate: a highly chiral cavity for enantiodiscrimination by NMR

A new chiral molecular tweezer, di-(R,R)-1-[10-(1-hydroxy-2,2,2-trifluoroethyl)-9-anthryl]-2,2,2-trifluoroethyl muconate 2, was synthesized in enantiopure form, and its geometry was studied using NMR and molecular mechanics. The effectiveness of 2 as a chiral solvating agent for determining the enantiomeric composition of chiral compounds using NMR was demonstrated, improving the results obtained with other methods. The stoichiometry and the association constant of the resulting diastereomeric complexes were studied, and their geometry was analyzed by NOE and 1H NMR.     

Synthesis of enantiopure substituted piperidines via an aziridinium ring expansion

Herein we report a novel methodology for the asymmetric synthesis of 3-substituted piperidines from readily available chiral building blocks. This method, which features a novel irreversible dihydropyrole-tetrahydropyridine ring expansion, allows the introduction of a large variety of substituents at the 3-position and permits substitution at the 2- and 6-position giving mono-, di-, or trisubstituted piperidines with high diastereocontrol.     

Two-component dendritic gel: effect of stereochemistry on the supramolecular chiral assembly

The self-assembly of diaminododecane solubilised by four different stereoisomeric dendritic peptides to form gel-phase materials in toluene was investigated. The second generation dendritic peptides were based on D- and L-lysine building blocks, and each contained three chiral centres. By designing dendritic peptides in which the configurations of the chiral centres were modified, and applying them as gelator units, the assembly of stereoisomers could be investigated. In all cases, the self-assembly of gelator units resulted in macroscopic gelation. However, the degree of structuring was modulated by the stereoisomers employed, an effect which changed the morphology and macroscopic behavior of the self-assembled state. Enantiomeric (L,L,L or D,D,D) gelator units formed fibrous molecular assemblies, whilst the racemic gel (50 % L,L,L : 50 % D,D,D) formed a flat structure with a "woven" appearance. Gelator units based on L,D,D or D,L,L dendritic peptides also formed fibrous assemblies, but small-angle X-ray scattering indicated significant morphological differences were caused by the switch in chirality. Furthermore, the macroscopic stability of the gel was diminished when these peptides were compared with their L,L,L or D,D,D analogues. In this paper it is clearly shown that individual stereocentres, on the molecular level, are directly related to the helicity within the fibre. It is argued that the chirality controls the pattern of hydrogen bonding within the assembly, and hence determines the extent of fibre formation and the macroscopic gel strength.