The role of dynamically correlated conformational equilibria in the folding of macromolecular structures. A model for the design of folded dendrimers

Light-triggered transformation of stilbene supramolecular polymers: thermodynamic versus kinetic control

Light irradiation of stilbene supramolecular polymers produces [2+2] cycloadducts in the kinetically trapped state, which convert to the thermodynamically favorable state upon thermal annealing due to the shift of hydrogen bonds from intra- to inter-complexation modes.

Tacticity dependence of single chain polymer folding

Precision polymerization techniques offer the exciting opportunity to manufacture single-chain nanoparticles (SCNPs) with intramolecular crosslinks placed in specific positions along the polymer chain.

Intramolecular hydrogen bond directed distribution of conformational populations in the derivatives of N′-benzylidenebenzohydrazide

The extensive NMR investigations reveal the presence of E-isomers in the derivative of N′-benzylidenebenzohydrazide. The different conformer populations are controlled by the strength of intramolecular hydrogen bonds.

Intramolecular hydrogen bond directed stable conformations of benzoyl phenyl oxalamides: unambiguous evidence from extensive NMR studies and DFT-based computations

A number of benzoyl phenyl oxalamide derivatives have been synthesized and characterized by the extensive utility of one- and two-dimensional NMR experimental techniques. The manifestation of intramolecular hydrogen bonds in all of the synthesized molecules, convincingly established using NMR studies, governs the stable conformations of the molecules. In the fluorine substituted molecules, the coupling between two NMR active nuclei mediated through hydrogen bonds has been detected. The measured chemical shift difference of an NH proton has been employed to calculate the energy of the HBs. NMR analysis revealed the electrostatic nature of the hydrogen bonds in all of the molecules. The NMR experimental findings have been validated using Density Functional Theory (DFT)-based Non Covalent Interactions (NCIs) and Quantum Theory of Atoms In Molecules (QTAIM) computations.

Intramolecular Hydrogen Bonding Involving Organic Fluorine: NMR Investigations Corroborated by DFT-Based Theoretical Calculations

The combined utility of many one and two dimensional NMR methodologies and DFT-based theoretical calculations have been exploited to detect the intramolecular hydrogen bond (HB) in number of different organic fluorine-containing derivatives of molecules, viz. benzanilides, hydrazides, imides, benzamides, and diphenyloxamides. The existence of two and three centered hydrogen bonds has been convincingly established in the investigated molecules. The NMR spectral parameters, viz., coupling mediated through hydrogen bond, one-bond NH scalar couplings, physical parameter dependent variation of chemical shifts of NH protons have paved the way for understanding the presence of hydrogen bond involving organic fluorine in all the investigated molecules. The experimental NMR findings are further corroborated by DFT-based theoretical calculations including NCI, QTAIM, MD simulations and NBO analysis. The monitoring of H/D exchange with NMR spectroscopy established the effect of intramolecular HB and the influence of electronegativity of various substituents on the chemical kinetics in the number of organic building blocks. The utility of DQ-SQ technique in determining the information about HB in various fluorine substituted molecules has been convincingly established.

Correlation between the Selectivity and the Structure of an Asymmetric Catalyst Built on a Chirally Amplified Supramolecular Helical Scaffold

For the first time, supramolecular helical rods composed of an achiral metal complex and a complementary enantiopure monomer provided a good level of enantioinduction in asymmetric catalysis. Mixtures containing an achiral ligand monomer (BTA(PPh2), 2 mol %) and an enantiopure ligand-free comonomer (ester BTA, 2.5 mol %), both possessing a complementary benzene-1,3,5-tricarboxamide (BTA) central unit, were investigated in combination with [Rh(cod)2]BArF (1 mol %) in the asymmetric hydrogenation of dimethyl itaconate. Notably, efficient chirality transfer occurs within the hydrogen-bonded coassemblies formed by BTA Ile and the intrinsically achiral catalytic rhodium catalyst, providing the hydrogenation product with up to 85% ee. The effect of the relative content of BTA Ile as compared to the ligand was investigated. The amount of chiral comonomer can be decreased down to one-fourth of that of the ligand without deteriorating the enantioselectivity of the reaction, while the enantioselectivity decreases for mixtures containing high amounts of BTA Ile. The nonlinear relationship between the amount of chiral comonomer and the enantioselectivity indicates that chirality amplification effects are at work in this catalytic system. Also, right-handed helical rods are formed upon co-assembly of the achiral rhodium complex of BTA(PPh2) and the enantiopure comonomer BTA Ile as confirmed by various spectroscopic and scattering techniques. Remarkably, the major enantiomer and the selectivity of the catalytic reaction are related to the handedness and the net helicity of the coassemblies, respectively. Further development of this class of catalysts built on chirally amplified helical scaffolds should contribute to the design of asymmetric catalysts operating with low amounts of chiral entities.

Intramolecular hydrogen bonds involving organic fluorine in the derivatives of hydrazides: an NMR investigation substantiated by DFT based theoretical calculations

The rare examples of intramolecular hydrogen bonds (HB) of the type the N-H∙∙∙F-C, detected in a low polarity solvent in the derivatives of hydrazides, by utilizing one and two-dimensional solution state multinuclear NMR techniques, are reported. The observation of through-space couplings, such as, (1h)JFH, and (1h)JFN, provides direct evidence for the existence of intra-molecular HB. Solvent induced perturbations and the variable temperature NMR experiments unambiguously establish the presence of intramolecular HB. The existence of multiple conformers in some of the investigated molecules is also revealed by two dimensional HOESY and (15)N-(1)H HSQC experiments. The (1)H DOSY experimental results discard any possibility of self or cross dimerization of the molecules. The derived NMR experimental results are further substantiated by Density Function Theory (DFT) based Non Covalent Interaction (NCI), and Quantum Theory of Atom in Molecule (QTAIM) calculations. The NCI calculations served as a very sensitive tool for detection of non-covalent interactions and also confirm the presence of bifurcated HBs.

Organic fluorine involved intramolecular hydrogen bonds in the derivatives of imides: NMR evidence corroborated by DFT based theoretical calculations

The rare occurrence of intramolecular hydrogen bonds (HBs) of the type N–H⋯F–C is detected in the derivatives of imides in a low polarity solvent by using multi-dimensional and multinuclear NMR experiments.

Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches

Based on integrative computational hybrid approaches that combined statistical coupling analysis (SCA), molecular dynamics (MD), and normal mode analysis (NMA), evolutionarily coupled residues involved in functionally relevant motion in the adenylate kinase protein family were identified. The hybrids identified four top-ranking site pairs that belong to a conserved hydrogen bond network that is involved in the enzyme's flexibility. A second group of top-ranking site pairs was identified in critical regions for functional dynamics, such as those related to enzymatic turnover. The high consistency of the results obtained by SCA with NMA (SCA.NMA) and by SCA.MD hybrid analyses suggests that suitable replacement of the matrix of cross-correlation analysis of atomic fluctuations (derived by using NMA) with those based on MD contributes to the identification of such sites by means of a fast computational calculation. The analysis presented here strongly supports the hypothesis that evolutionary forces, such as coevolution at the sequence level, have promoted functional dynamic properties of the adenylate kinase protein family. Finally, these hybrid approaches can be used to identify, at the residue level, protein motion coordination patterns not previously observed, such as in hinge regions.

N-H...F hydrogen bonds in fluorinated benzanilides: NMR and DFT study

Using (19)F and (1)H-NMR (with (14)N decoupling) spectroscopic techniques together with density functional theoretical (DFT) calculations, we have investigated weak molecular interactions in isomeric fluorinated benzanilides. Simultaneous presence of through space nuclear spin-spin couplings ((1h)J(N-HF)) of diverse strengths and feeble structural fluctuations are detected as a function of site specific substitution of fluorine atoms within the basic identical molecular framework. The transfer of hydrogen bonding interaction energies through space is established by perturbing their strengths and monitoring the effect on NMR parameters. Multiple quantum (MQ) excitation, up to the highest possible MQ orders of coupled protons, is utilized as a tool for accurate (1)H assignments. Results of NMR studies and DFT calculations are compared with the relevant structural parameters taken from single crystal X-ray diffraction studies.

Amplification of local chirality within a folded dendrimer. An intramolecular ‘sergeants and soldiers’ experiment

A series of pyridine-2,6-dicarboxamide dendrons having varying proportions of chiral and achiral termini have been prepared. Circular dichroism and X-ray crystallographic studies indicate that these folded dendrons propagate terminal chirality via a ‘sergeants and soldiers’ process. The extent of chiral amplification shows a dependence on dendron generation, but also is affected by the relative positioning of the chiral termini at the periphery of the dendron. Analysis of the crystal structures of the G1 dendrons, 4a – 6a , reveals chain–chain and chain–dendron conformational communication, which is likely to be responsible for the chiral amplification observed in solution.

Glycopeptide dendrimers, part III: a review. Use of glycopeptide dendrimers in immunotherapy and diagnosis of cancer and viral diseases

Glycopeptide dendrimers containing different types of tumor associated-carbohydrate antigens (T(N), TF, sialyl-T(N), sialyl-TF, sialyl-Le(x), sialyl-Le(a) etc.) were used in diagnosis and therapy of different sorts of cancer. These dendrimeric structures with incorporated T-cell epitopes and adjuvants can be used as antitumor vaccines. Best results were obtained with multiantigenic vaccines, containing, e.g. five or six different TAAs. The topic of TAAs and their dendrimeric forms at molecular level are reviewed, including structure, syntheses, and biological activities. Use of glycopeptide dendrimers as antiviral vaccines against HIV and influenza is also described. Their syntheses, physico-chemical properties, and biological activities are given with many examples.

Temperature-induced chiroptical changes in a helical poly(phenylacetylene) bearing N,N-diisopropylaminomethyl groups with chiral acids in water

A stereoregular poly(phenylacetylene) bearing an N,N-diisopropylaminomethyl group as the pendant (poly-1) changed its structure into the prevailing one-handed helical conformation upon complexation with optically active acids in water. The complexes exhibited induced circular dichroism (ICD) in the UV/Vis region of the polymer backbone. Poly-1 is highly sensitive to the chirality of chiral acids and can detect a small enantiomeric imbalance in these acids, in particular, phenyl lactic acid in water. For example, a 0.005% enantiomeric excess of phenyl lactic acid can be detected by CD spectroscopy. The observed ICD intensity and pattern of poly-1 were dependent on the temperature and concentration of poly-1, probably due to aggregations of the polymer at high temperature as revealed by dynamic light scattering and AFM. On the basis of the temperature-dependent ICD changes, the preferred chiral helical sense of poly-1 was found to be controlled by noncovalent bonding interactions by using structurally different enantiomeric acids.

Strong Stacking between F⋅⋅⋅HN Hydrogen-Bonded Foldamers and Fullerenes: Formation of Supramolecular Nano Networks

The stacking interactions between FH--N hydrogen-bonded foldamers 1-3, bis-foldamer 4, and tris-foldamer 5 and C(60) and C(70) are described. Compound 4 contains two folded units, which are connected by an isophthalamide linker, whereas 5 has a C(3)-symmetrical discotic structure, in which three folded units are connected by a benzene-1,3,5-tricarboxamide unit. UV/Vis, fluorescence, and NMR experiments have revealed that the foldamers or folded units strongly stack with fullerenes in chloroform. The (apparent) association constants of the respective complexes have been determined by a fluorescence titration method. The strong association is tentatively attributed to intermolecular cooperative fluorophenylpi and solvophobic interactions. A similar but weaker interaction has also been observed between an MeOH--N hydrogen-bonded foldamer and fullerenes. AFM studies have revealed that the surfaces of 3 and 4 show fibrous networks, while the surface of 5 shows particles. In sharp contrast, mixtures of 3 and 4 with C(60) have been shown to generate thinner separated fibrils, whereas a mixture of 5 and C(60) produces honeycomb-like nano networks, for which a columnar cooperative stacking pattern is proposed. The results demonstrate the usefulness of FH--N hydrogen-bonded folded structures in the construction of nanoscaled materials.

Expanding Dendrons. The Photoisomerism of Folded Azobenzene Dendrons

Irradiation of a folded azobenzene dendron system triggers a large, reversible structural expansion. The dendrons adopt a compact helical conformation in the stable E form owing to the E geometry of azo linkage and the syn-syn preference of the dendritic branch points. E --> Z photoisomerization disrupts this folded conformation in a manner that decreases the packing efficiency and results in an expansion in hydrodynamic volume.

Helical Conformational Dynamics and Photoisomerism of Alternating Pyridinedicarboxamide/m-(Phenylazo)azobenzene Oligomers

Alternating sequences of pyridine-2,6-dicarboxamides and meta-(phenylazo)azobenzenes have been assembled into oligomers composed of four (8) and eight (9) azobenzene linkages. X-ray crystallography confirmed that oligomer 8 adopts a two-turn helical conformation with a helical pitch of approximately 3.4 Angstroms in the solid state. The presence of a two- and four-turn helical conformation of 8 and 9, respectively, in polar and nonpolar solvents was elucidated by the anisotropic upfield shifting of protons located within the helices, NOE enhancements between protons oriented toward the helix interior, and the diastereotopicity of the terminal benzyloxycarbonyl (CBz) methylene protons. (1)H NMR line shape analysis of the CBz methylene hydrogens at the chain ends revealed a dynamic equilibria interconverting M and P helical conformations with energetic barriers (DeltaG) of 11.1 (DeltaS = -19.4 +/- 1.6 cal mol(-1) K(-1); DeltaH = 6.5 +/- 0.4 kcal/mol) for 8 and 13.8 kcal/mol (DeltaS = -6.6 +/- 6.2 cal mol(-1) K(-1); DeltaH = 11.8 +/- 1.8 kcal/mol) for 9. Irradiation of the oligomers with 350 nm light induces an E --> Z isomerization of the azo linkages that decreases in efficacy at longer helix lengths. The suppression of E --> Z isomerization is a consequence of the contrasting behavior of the azo linkages located at the helix termini, which afford Z/E ratios similar to those of model compound 7d, and the internal azo groups, which undergo significantly lower Z/E conversion ratios compared with 7e.