Quantitative determination of intermolecular interactions with fluorinated aromatic rings

A role of intermolecular interaction modulating thermal diffusivity in organosuperelastic and organoferroelastic cocrystals

Although the finding of superelasticity and ferroelasticity in organic crystals has been serendipitous, an increasing number of organic crystals with such deformation properties have been witnessed. Understanding the structure-property relationship can aid in the rational selection of intermolecular interactions to design organic crystals with desired superelastic or ferroelastic properties. In this study, we investigated the mechanical deformation in two cocrystals, prepared with the parent compound, 1,4-diiodotetrafluorobenzene with two coformers, 1,2-bis(4-pyridyl)ethane and pyrene. The parent compound and coformers were chosen to introduce distinct weak interactions such as halogen bonds and C-H⋯F, and π⋯π interactions in the crystal structure. The two cocrystals exhibited different mechanical deformations, superelasticity, and ferroelasticity, respectively. The single-crystal X-ray diffraction and energy framework analysis of the crystal structure of the cocrystals revealed that both deformations were caused by mechanical twinning. Interestingly, a difference in the extent of deformation was observed, modulated by a combination of strong and weak intermolecular interactions in the superelastic cocrystal, and only weak interaction in the ferroelastic one. In this comparison, the superelastic cocrystal exhibited higher thermal diffusivity than the ferroelastic cocrystal, indicating the presence of symmetrical and relatively robust intermolecular interactions in the superelastic cocrystal.

Substituent effects on aromatic interactions in water

Molecular recognition in water involves contributions due to polar functional group interactions, partial desolvation of polar and non-polar surfaces and changes in conformational flexibility, presenting a challenge for rational design and interpretation of supramolecular behaviour. Conformationally well-defined supramolecular complexes that can be studied in both water and non-polar solvents provide a platform for disentangling these contributions. Here 1 : 1 complexes formed between four different calix[4]pyrrole receptors and thirteen different pyridine N-oxide guests have been used to dissect the factors that govern substituent effects on aromatic interactions in water. H-bonding interactions between the receptor pyrrole donors and the guest N-oxide acceptor at one end of the complex lock the geometrical arrangement of a cluster of aromatic interactions at the other end of the complex, so that a phenyl group on the guest makes two edge-to-face and two stacking interactions with the four aromatic side-walls of the receptor. The thermodynamic contribution of these aromatic interactions to the overall stability of the complex was quantified by chemical double mutant cycles using isothermal titration calorimetry and ¹H NMR competition experiments. Aromatic interactions between the receptor and a phenyl group on the guest stabilise the complex by a factor of 1000, and addition of substituents to the guest phenyl group further stabilises the complex by an additional factor of up to 1000. When a nitro substituent is present on the guest phenyl group, the complex has a sub-picomolar dissociation constant (370 fM). The remarkable substituent effects observed in water for these complexes can be rationalised by comparison with the magnitude of the corresponding substituent effects measured in chloroform. In chloroform, the double mutant cycle free energy measurements of the aromatic interactions correlate well with the substituent Hammett parameters. Electron-withdrawing substituents increase the strength of the interactions by a factor of up to 20, highlighting the role of electrostatics in stabilising both the edge-to-face and stacking interactions. The enhanced substituent effects observed in water are due to entropic contributions associated with the desolvation of hydrophobic surfaces on the substituents. The flexible alkyl chains that line the open end of the binding site assist the desolvation of the non-polar π-surfaces of polar substituents, like nitro, but at the same time allow water to interact with the polar H-bond acceptor sites on the substituent. This flexibility allows polar substituents to maximise non-polar interactions with the receptor and polar interactions with the solvent, leading to remarkably high binding affinities.

Copolymers Derived from Two Active Esters: Synthesis, Characterization, Thermal Properties, and Reactivity in Post-Modification

Copolymers with two distinguished reactive repeating units are of great interest, as such copolymers might open the possibility of obtaining selective and/or consequent copolymers with different chemical structures and properties. In the present work, copolymers based on two active esters (pentafluorophenyl methacrylate and p-nitrophenyl methacrylate) with varied compositions were synthesized by Cu(0)-mediated reversible deactivation radical polymerization. This polymerization technique allows the preparation of copolymers with high to quantitative conversion of both comonomers, with moderate control over dispersity (Đ = 1.3–1.7). Additionally, by in-depth study on the composition of each copolymer by various techniques including elemental analysis, NMR, FT-IR, and XPS, it was possible to confirm the coherence between expected and obtained composition. Thermal analyses by DSC and TGA were implemented to investigate the relation between copolymers’ composition and their thermal properties. Finally, an evaluation of the difference in reactivity of the two monomer moieties was confirmed by post-modification of copolymers with a primary amine and a primary alcohol as the model.

New insights into progressive ligand replacement from [Ru2Cl(O2CCH3)4]: synthetic strategies and variation in redox potentials and paramagnetic shifts

The complete series of [Ru₂Cl(Dp-FPhF)_x(O₂CCH₃)_4-x] (x = 1-4; Dp-FPhF^- = N,N'-bis(4-fluorophenyl)formamidinate) compounds, has been prepared and characterized by a multi-technique approach, including single crystal X-ray diffraction. A careful study of the different methodologies has allowed us to prepare four compounds with good yields and without an inert atmosphere or further purification. Specifically, [Ru₂Cl(Dp-FPhF)(O₂CCH₃)₃] (1) was obtained using an ultrasound-assisted (USS) method, while [Ru₂Cl(Dp-FPhF)₄] (4) was prepared by microwave assisted solvothermal synthesis (MWS). The intermediate substitution products cis-[Ru₂Cl(Dp-FPhF)₂(O₂CCH₃)₂] (2) and [Ru₂Cl(Dp-FPhF)₃(O₂CCH₃)] (3) have been prepared by conventional heating, controlling the molar ratio of the starting materials. ESI-MS and infrared spectroscopy were used to follow all the reactions and permitted a qualitative evaluation of the axial reactivity in this series. Magnetic and absorption measurements confirmed a high spin σ²π⁴δ²(π*δ*)³ electronic configuration in all cases. However, the effect of the gradual modification of the electronic density in the diruthenium core markedly affects other properties. The cyclic voltammograms of the compounds show a strong decrease in the one electron oxidation potential and an increase in the reduction potential in the series from 1 to 4. Furthermore, despite their paramagnetic nature, ¹H- and ¹⁹F-NMR spectra were recorded, and a correlation between the paramagnetic shift of the signals and the substitution degree of the diruthenium species was observed. These results provide a comprehensive guide to synthesise and understand the effects of equatorial ligand substitution on the properties of Ru₂⁵⁺ compounds.

Effect of Hydrogen Bonds and π...π-interactions on the Crystallization of Phenyl-perfluorophenyl Amides: Understanding the Self-organization of a Cocrystal

A series of N-arylbenzamides containing amide group and phenyl−perfluorinated rings were used as the smallest molecules to investigate the direct influence of hydrogen bond and aromatic donor-acceptor complementarity in the...

Arene-Perfluoroarene Interactions in Solution

A systematic study of arene-perfluoroarene interactions in solution is presented. Using a combination of NMR titration experiments, X-ray crystallography, and computational analysis, we analyze the effects of fluorination, substituents, ring size, and solvation on the arene-perfluoroarene interaction. We find that fluorination, extension of the π systems, and enhancement of solvent polarity greatly stabilize the stacking energy up to 3 orders of magnitude (K_a = <1 to 6000 M^-1), with the highest K_a achieved for the interaction of water-soluble variants of perfluoronaphthalene and anthracene in buffered D₂O (pD = 12). Combining computational and experimental results, we conclude that this impressive binding energy is a result of enthalpically favorable electrostatic and dispersion interactions as well as the entropically driven hydrophobic effect. The enhanced understanding of arene-perfluoroarene interactions in aqueous solution sets the stage for the implementation of this abiotic intermolecular interaction in biology and medicine.

Regulating the reactivity of black phosphorus via protective chemistry

Rationally regulating the reactivity of molecules or functional groups is common in organic chemistry, both in laboratory and industry synthesis. This concept can be applied to inorganic nanomaterials, particularly two-dimensional black phosphorus (BP) nanosheets. The high reactivity of few-layer (even monolayer) BP is expected to be "shut down" when not required and to be resumed upon application. Here, we demonstrate a protective chemistry-based methodology for regulating BP reactivity. The protective step initiates from binding Al³⁺ with lone pair electrons from P to decrease the electron density on the BP surface, and ends with an oxygen/water-resistant layer through the self-assembly of hydrophobic 1,2-benzenedithiol (BDT) on BP/Al³⁺ This protective step yields a stabilized BP with low reactivity. Deprotection of the obtained BP/Al³⁺/BDT is achieved by chelator treatment, which removes Al³⁺ and BDT from the BP surface. The deprotective process recovers the electron density of BP and thus restores the reactivity of BP.

Halogenated isophthalamides and dipicolineamides: the role of the halogen substituents in the anion binding properties

A novel family of amide-based receptors is herein described. Specifically, the role of the halogen substituents at the aryl moieties in the anion binding properties of a series of halogenated isophthalamides and dipicolineamides (L1-L6) was investigated both in solution and in the solid state in order to evaluate the incidence of all possible different and combined weak host-guest interactions. Only L5 and L6 bearing pentafluorophenyl rings as substituents have some affinities for the set of anions studied. In particular, in the case of L5 an interesting behaviour with the formation of a non-symmetric adduct with benzoate and dihydrogen phosphate was hypothesised by ¹H- and ¹⁹F-NMR spectroscopy studies in solution and confirmed by theoretical calculation. The study of the crystal structures of the receptors demonstrated that the steric hindrance determined by the halogen substituents in the receptor molecules influences the accessibility of the anions to the isophthalamide or dipicoline amide NH moieties, thus modulating the affinity for the anion guests.

Columnar Stacking of Partially Fluorinated [4]Helicenes: C-H⋅⋅⋅F Interactions Change the Stacking Orientation

The partial fluorination of polycyclic aromatic hydrocarbons often produces a layered crystal packing, where fluorinated aromatic surfaces are stacked over nonfluorinated aromatic surfaces. Herein, we report the synthesis and crystal packing of partially fluorinated [4]helicenes with steric congestion resulting from H and F atoms in the fjord region. F₆ -[4]Helicene forms head-to-tail columnar stacks consisting of an alternate arrangement of perfluorinated and nonfluorinated naphthalene moieties. With decreasing fluorine content, aromatic stacking switched from arene-fluoroarene (Ar^H -Ar^F ) hetero-stacking to Ar^H -Ar^H /Ar^F -Ar^F homo-stacking with the help of intermolecular C-H⋅⋅⋅F contacts in the fjord region. As a result, head-to-head columnar stacks appear. Therefore, the conventional Ar^H -Ar^F stacking motif is not always applicable to F_n -[4]helicenes with twisted π-surfaces.

Unraveling the unusual effect of fluorination on crystal packing in an organic semiconductor

Owing to combination of chemical and thermal stability, favorable molecular packing, and efficient electron transport, naphthalene diimide derivatives (NDIs) are promising materials for n-channel organic field effect transistors (OFETs). For tuning the properties of n-conductive organic semiconductors, as well as for improvement of their air stability, fluorination is a frequently used approach. In this study, we demonstrate how very small modification of the molecular structure - fluorine substitution in the p-position of the phenyl rings of N,N'-diphenyl-NDI (Ph-NDI) - dramatically changes the crystal packing but almost does not affect electron transport. We show that this two-atom modification of Ph-NDI changes the molecular packing motif from π-stacking to a herringbone one, in contrast with usually observed improvement of π-stacking with fluorination. This unexpected behavior is mainly attributed to changes in the electrostatic potential of the phenyl rings as a result of fluorination, which alters their relative orientation and modifies the packing of the NDI cores. Nevertheless, though the herringbone packing is typically considered as less favorable for charge transport, the theoretical electron mobility is slightly higher in the fluorinated Ph-NDI. The results obtained improve the understanding of the relationship between the molecular and crystal structures of organic semiconductors and their impact on charge transport, which is of key importance for rational design of high-mobility materials for organic electronics.

Impact of N-substitution on structural, electronic, optical, and vibrational properties of a thiophene–phenylene co-oligomer

Properties of the organic semiconductors can be finely tuned via changes in their molecular structure.

Supramolecular synthons in fluorinated benzyl nitrophenyl sulfides

An entangled gauche-conformation in 4-nitrophenyl pentafluorobenzyl sulfide and its “fingerprint analysis”.

Impact of molecular packing rearrangement on solid-state fluorescence: polyhalogenated N-hetarylamines vs. their co-crystals with 18-crown-6

Relationship between the hetarylamine chemical structure, crystal packing in homo- and co-crystals, and fluorescence effects (quenching, bathochromic and hypsochromic shifts).

Experimental Binding Energies in Supramolecular Complexes

On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.

Ligand-Enabled, Copper-Promoted Regio- and Chemoselective Hydroxylation of Arenes, Aryl Halides, and Aryl Methyl Ethers

We report here a practical method for the ortho C-H hydroxylation of benzamides with inexpensive copper(II) acetate monohydrate and a pyridine ligand. An intra- and intermolecular ligand combination was explored to achieve regio- and chemoselective hydroxylation. Interestingly, typical regiochemical scrambling associated with the C-H activation was further resolved by introducing a ligand-directed ortho hydroxylation of haloarenes and aryl methyl ethers.

High Glass Transition Temperature Fluoropolymers for Hydrophobic Surface Coatings via RAFT Copolymerization

The preparation of polymer thin films or surface coatings that display a static water contact angle >95° often requires hierarchical roughness features or surface functionalization steps. In addition, inherently hydrophobic polymers such as fluoropolymers often possess low glass transition temperatures, reducing their application where thermal stability is required. Herein, the first reported synthesis of 2,3,4,5,6-pentafluorostyrene (PFS) and N-phenylmaleimide (NMI) via reversible addition–fragmentation chain-transfer (RAFT)-mediated free radical polymerization is presented, with a view towards the preparation of inherently hydrophobic polymers with a high glass transition temperature. A suite of copolymers were prepared and characterized, and owing to the inherent rigidity of the maleimide group in the polymer backbone and π–π interactions between adjacent PFS and NMI groups, very high glass transition temperatures were achieved (up to 180°C). The copolymerization of N-pentafluorophenylmaleimide was also performed, also resulting in extremely high glass transition temperature copolymers; however, these polymers did not exhibit characteristics of being under RAFT control. Thin films of PFS-NMI copolymers exhibited a static contact angle ~100°, essentially independent of the amount of NMI incorporated into the polymer.

Theoretical study of intermolecular interactions in crystalline arene–perhaloarene adducts in terms of the electron density

The intermolecular interactions in C₆X₆–arene crystals (X = F, Cl) and the halogen substitution effect can be quantified by the electron density.

cis and trans influences on [Pt(SRF)(triphos)]+ complexes (SRF = polyfluorobenzothiolate)

Platinum(ii) derivatives of the tridentate ligand Ph₂PCH₂CH₂P(Ph)CH₂CH₂PPh₂ (triphos), including [Pt(SR_F)(triphos)](CF₃SO₃) R_F = C₆F₄CF₃-4 1, C₆F₅2, C₆HF₄-4 3, C₆H₄CF₃-4 4, C₆H₃F₂-2,4 5, C₆H₄F-2 6, C₆H₄F-4 7 and C₆H₅8, have been prepared and characterised.

Biophysical methods in drug discovery from small molecule to pharmaceutical

Biophysical methods have become established in many areas of drug discovery. Application of these methods was once restricted to a relatively small number of scientists using specialized, low throughput technologies and methods. Now, automated high-throughput instruments are to be found in a growing number of laboratories. Many biophysical methods are capable of measuring the equilibrium binding constants between pairs of molecules crucial for molecular recognition processes, encompassing protein-protein, protein-small molecule, and protein-nucleic acid interactions, and several can be used to measure the kinetic or thermodynamic components controlling these biological processes. For a full characterization of a binding process, determinations of stoichiometry, binding mode, and any conformational changes associated with such interactions are also required. The suite of biophysical methods that are now available represents a powerful toolbox of techniques which can effectively deliver this full characterization.The aim of this chapter is to provide the reader with an overview of the drug discovery process and how biophysical methods, such as surface plasmon resonance (SPR), isothermal titration calorimetry (ITC), nuclear magnetic resonance, mass spectrometry (MS), and thermal unfolding methods can answer specific questions in order to influence project progression and outcomes. The selection of these examples is based upon the experiences of the authors at AstraZeneca, and relevant approaches are highlighted where they have utility in a particular drug discovery scenario.

Experimental evaluation of CH-π interactions in a protein core

CH-π stacks up! Using the protein α(2) D as a model system, we estimate that a CH-π contact between cyclohexylalanine (Cha) and phenylalanine (F) contributes approximately -0.7 kcal  mol(-1) to the protein stability. The stacking F-Cha pairs are sequestered in the core of the protein, where water interference does not exist (see figure). Therefore, the observed energetic gain should represent the inherent magnitude and upper limit of the CH-π interactions.

Aromatic rings in chemical and biological recognition: energetics and structures

This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.

Solid-state [2+2] photodimerization and photopolymerization of α,ω-diarylpolyene monomers: effective utilization of noncovalent intermolecular interactions in crystals

[2+2] Photocycloaddition of olefins is a very useful reaction in synthetic organic chemistry to obtain cyclobutane-containing molecules, which are almost inaccessible by other methods. The reaction, when performed in the crystalline state, occurs more efficiently and selectively than in homogeneous solution due to tight and regular molecular arrangement in the crystal state. Despite numerous examples for the solid-state [2+2] photodimerization of monoenes, however, it is still a challenge to prepare not only dimers but also higher oligomers and polymers from conjugated polyenes, which have multiple reactive double bonds in a molecule. In our recent studies of the solid-state photoreactions of α,ω-diarylpolyenes, noncovalent intermolecular interactions in crystals were effectively utilized to prealign molecules in stacking arrangements, suitable for the [2+2] reaction. With appropriate ring-substituents, [2+2] photodimerization and photopolymerization of the polyenes took place, although the degree of polymerization was relatively low. This review will describe the details of these reactions.

Binding mechanisms in supramolecular complexes

Supramolecular chemistry has expanded dramatically in recent years both in terms of potential applications and in its relevance to analogous biological systems. The formation and function of supramolecular complexes occur through a multiplicity of often difficult to differentiate noncovalent forces. The aim of this Review is to describe the crucial interaction mechanisms in context, and thus classify the entire subject. In most cases, organic host-guest complexes have been selected as examples, but biologically relevant problems are also considered. An understanding and quantification of intermolecular interactions is of importance both for the rational planning of new supramolecular systems, including intelligent materials, as well as for developing new biologically active agents.

Halogenated ligands and their interactions with amino acids: implications for structure-activity and structure-toxicity relationships

The properties of chemicals are rooted in their molecular structure. It follows that structural analysis of specific interactions between ligands and biomolecules at the molecular level is invaluable for defining structure-activity relationships (SARs) and structure-toxicity relationships (STRs). This study has elucidated the structural and molecular basis of interactions of biomolecules with alkyl and aryl halides that are extensively used as components in many commercial pesticides, disinfectants, and drugs. We analyzed the protein structures deposited in Protein Data Bank (PDB) for structural information associated with interactions between halogenated ligands and proteins. This analysis revealed distinct patterns with respect to the nature and structural characteristics of halogen interactions with specific types of atoms and groups in proteins. Fluorine had the highest propensity of interactions for glycine, while chlorine for leucine, bromine for arginine, and iodine for lysine. Chlorine, bromine and iodine had the lowest propensity of interactions for cysteine, while fluorine had a lowest propensity for proline. These trends for highest propensity shifted towards the hydrophobic residues for all the halogens when only interactions with the side chain were considered. Halogens had equal propensities of interaction for the halogen bonding partners (nitrogen and oxygen atoms), albeit with different geometries. The optimal angle for interactions with halogens was approximately 120 degrees for oxygen atoms, and approximately 96 degrees for nitrogen atoms. The distance distributions of halogens with various amino acids were mostly bimodal, and the angle distributions were unimodal. Insights gained from this study have implications for the rational design of safer drugs and commercially important chemicals.

Aggregation of ionic liquids [C(n)mim]Br (n = 4, 6, 8, 10, 12) in D2O: a NMR study

Aqueous solutions of five ionic liquids (ILs) of the 1-n-alkyl-3-methylimidazolium bromide family, [C(n)mim]Br (n = 4, 6, 8, 10, 12), were investigated by NMR measurements at 298.2 K as a function of IL concentrations. Critical aggregation concentrations and aggregation numbers of these ILs were determined by 1H NMR except for [C4mim]Br in D2O. The effects of the alkyl chain length of the cations were examined on the aggregation behavior of the ILs. 1H NMR data of the solvent D2O were used to investigate the hydration of the ILs in D2O, and it was found that the ionic hydration and the cation-anion association or aggregation of the ILs offset each other. The microenvironment of different protons of cations of the ILs in the aggregates was probed by determining the spin-lattice relaxation rate (1/T1). It is suggested that the imidazolium rings in the aggregates are exposed to water and that the molecular motion of the aggregates is more restricted than that of the monomers of the ILs. Furthermore, a stair-like microscopic aggregation structure is suggested for the [C(n)mim]Br/D2O (n = 6, 8, 10) systems from 2-D 1H-1H NOESY measurements.

Fluorinated diphenylpolyenes: crystal structures and emission properties

(E,E,E)-1,6-Diaryl(Ar)-1,3,5-hexatrienes (2, Ar = 4-fluorophenyl; 3, Ar = 2,4-difluorophenyl; 4, Ar = 2,4,6-trifluorophenyl; 5, Ar = perfluorophenyl) and (E,E,E)-1-perfluorophenyl-6-phenyl-1,3,5-hexatriene (6) were prepared. The absorption and fluorescence spectra in methylcyclohexane solution showed only a small dependence on the fluorine ring substituent, and were similar to those of the unsubstituted parent compound (1, Ar = phenyl). The solid-state absorption and fluorescence spectra shifted to red relative to those in solution and strongly depended on the substituent. The emission from crystals 1-5 originated mainly from monomeric species with the maximum wavelength (lambda f(max)) of 440-465 nm, which overlapped the emission from molecular aggregates (1-4) or excimeric species (5) in the red region. Crystal 6 exhibited red-shifted (lambda f(max) = 530 nm) and structureless emission due to excimers. The cocrystal of 1 and 5 (1/5) showed red-shifted (lambda f(max) = 558 nm) and distinctly structured emission, not from exciplexes but from the excited states of molecular aggregates in which molecules 1 and 5 strongly interact already in the ground state. These assignments were confirmed by the results of fluorescence lifetime and quantum yield measurements in the solid state. Single-crystal X-ray structure analyses showed that the molecules were basically planar in each crystal, whereas the crystal packing was strongly substituent-dependent. Weak pi-pi interactions in the herringbone (1 and 2) and in the pi-stacked but largely offset structures (3 and 4) account for their predominantly monomeric origin of emission. The observation of excimer fluorescence from 5 was rather unexpected, since the molecules in this crystal were arranged in an offset stacking fashion due to perfluorophenyl-perfluorophenyl (C6F5...C6F5) interaction. The structures of 6 and 1/5 considerably resembled each other, in which molecules were pi-stacked with more face-to-face geometries than those in 5, as a result of strongly attractive perfluorophenyl-phenyl (C6F5...C6H5) interaction. Nevertheless, the fluorescence origin was clearly different for 6 and 1/5. This can be ascribed to the difference in the strength of orbital-orbital interaction between molecular pi-planes in the ground and excited states in crystals.

X-ray diffraction and theoretical studies for the quantitative assessment of intermolecular arene-perfluoroarene stacking interactions

The arene-perfluoroarene stacking interaction was studied by experimental and theoretical methods. A series of compounds with different possibilities for formation of this recognition motif in the solid state were synthesized, and their crystal structures determined by single-crystal X-ray diffraction. The crystal packing of these compounds, as well as the packing of related compounds retrieved from crystallographic databases, were analyzed with quantitative crystal potentials: total lattice energies and the cohesive energies of closest molecular pairs in the crystals were calculated. The arene-perfluoroarene recognition motif emerges as a dominant interaction in the non-hydrogen-bonding compounds studied here, to the point that asymmetric dimers formed over the stacking motif carry over to asymmetric units made of two molecules in the crystal both for pure compounds and for molecular complexes; however, inter-ring distances and angles range from 3.70 to 4.85 A and from 5 to 21 degrees , respectively. Pixel energy partitioning reveals that whenever aromatic rings stack, the largest cohesive energy contribution comes from dispersion, which roughly amounts to 20 kJ mol(-1) per phenyl ring, while the coulombic term is minor but significant enough to make a difference between the arene-arene or perfluoroarene-perfluoroarene interactions on the one hand, and arene-perfluoroarene interactions on the other, whereby the latter are favored by about 10 kJ mol(-1) per phenyl ring. No evidence of special interaction which can be attributed to HF confrontation was recognizable.

Substituent effects on aromatic stacking interactions

Synthetic supramolecular zipper complexes have been used to quantify substituent effects on the free energies of aromatic stacking interactions. The conformational properties of the complexes have been characterised using NMR spectroscopy in CDCl(3), and by comparison with the solid state structures of model compounds. The structural similarity of the complexes makes it possible to apply the double mutant cycle method to evaluate the magnitudes of 24 different aromatic stacking interactions. The major trends in the interaction energy can be rationalised using a simple model based on electrostatic interactions between the pi-faces of the two aromatic rings. However, electrostatic interactions between the substituents of one ring and the pi-face of the other make an additional contribution, due to the slight offset in the stacking geometry. This property makes aromatic stacking interactions particularly sensitive to changes in orientation as well as the nature and location of substituents.

Enthalpy (DeltaH) and entropy (DeltaS) for pi-stacking interactions in near-sandwich configurations: relative importance of electrostatic, dispersive, and charge-transfer effects

Interactions between two aromatic rings with various substituents in a near-sandwich configuration have been quantitatively studied by using the triptycene derived molecular models. This model system allows a stacking arrangement of two arenes to assume a near-perfect face-to-face configuration in its ground state conformation. Comparing to our previous study of the parallel displaced configuration, repulsive interactions are predominant for most arenes currently studied. However, if one arene is strongly electron deficient (Ar2=pentafluorobenzoate), attractive interactions were observed regardless of the character of the other arene (Ar1). For stacking interactions between Me2NC6H4 and C6F5CO groups, a DeltaH of -1.84+/-0.2 kcal/mol and a DeltaS of -2.9+/-0.8 cal/(mol.K) were determined. The general trend in the attractive stacking interaction toward a pentafluorobenzoate is Me2NC6H4>Me3C6H2>Me2C6H3>MeC6H4>MeOC6H4>C6H5>O2NC6H4. The observed trend is consistent with a donor-acceptor relationship and the acceptor is a C6F5CO group.

Chemical double-mutant cycles: dissecting non-covalent interactions

Thermodynamic double-mutant cycles and triple-mutant boxes are widely employed for the experimental quantification of non-covalent interactions and cooperative effects in proteins. This review describes the application of these powerful methodologies to the study of non-covalent interactions in synthetic systems.

19F NMR studies of solvent exposure and peptide binding to an SH3 domain

(19)F NMR was used to study topological features of the SH3 domain of Fyn tyrosine kinase for both the free protein and a complex formed with a binding peptide. Metafluorinated tyrosine was biosynthetically incorporated into each of 5 residues of the G48M mutant of the SH3 domain (i.e. residues 8, 10, 49 and 54 in addition to a single residue in the linker region to the C-terminal polyhistidine tag). Distinct (19)F NMR resonances were observed and subsequently assigned after separately introducing single phenylalanine mutations. (19)F NMR chemical shifts were dependent on protein concentration above 0.6 mM, suggestive of dimerization via the binding site in the vicinity of the tyrosine side chains. (19)F NMR spectra of Fyn SH3 were also obtained as a function of concentration of a small peptide (2-hydroxynicotinic-NH)-Arg-Ala-Leu-Pro-Pro-Leu-Pro-diaminopropionic acid -NH(2), known to interact with the canonical polyproline II (PPII) helix binding site of the SH3 domain. Based on the (19)F chemical shifts of Tyr8, Tyr49, and Tyr54, as a function of peptide concentration, an equilibrium dissociation constant of 18 +/- 4 microM was obtained. Analysis of the line widths suggested an average exchange rate, k(ex), associated with the peptide-protein two-site exchange, of 5200 +/- 600 s(-1) at a peptide concentration where 96% of the FynSH3 protein was assumed to be bound. The extent of solvent exposure of the fluorine labels was studied by a combination of solvent isotope shifts and paramagnetic effects from dissolved oxygen. Tyr54, Tyr49, Tyr10, and Tyr8, in addition to the Tyr on the C-terminal tag, appear to be fully exposed to the solvent at the metafluoro position in the absence of binding peptide. Tyr54 and, to some extent, Tyr10 become protected from the solvent in the peptide bound state, consistent with known structural data on SH3-domain peptide complexes. These results show the potential utility of (19)F-metafluorotyrosine to probe protein-protein interactions in conjunction with paramagnetic contrast agents.