Aromatic interactions in model systems

Hairpin structure of a biarsenical-tetracysteine motif determined by NMR spectroscopy

The biarsenical-tetracysteine motif is a useful tag for genetic labeling of proteins with small molecules in living cells. The present study concerns the structure of a 12 amino acid peptide FLNCCPGCCMEP bound to the fluorophore ReAsH based on resorufin. (1)H NMR spectroscopy was used to determine the solution structure of the complex formed between the peptide and the ReAsH moiety. Structure calculations based on the NMR results showed that the backbone structure of the peptide is fairly well defined, with a hairpinlike turn, similar to a type-II beta-turn, formed by the central CPGC segment. The most stable complex was formed when As2 was bonded to C4 and C5 and As1 to C8 and C9. Two clear NOESY cross-peaks between the Phe1 side chain and ReAsH confirmed the close positioning of the phenyl ring of Phe1 and ReAsH. Phe1 was found to have an edge-face geometry relative to ReAsH. The close interaction between Phe1 and ReAsH may be highly significant for the fluorescence properties of the ReAsH complex.

Molecular mechanics of the alpha-actinin rod domain: bending, torsional, and extensional behavior

α-Actinin is an actin crosslinking molecule that can serve as a scaffold and maintain dynamic actin filament networks. As a crosslinker in the stressed cytoskeleton, α-actinin can retain conformation, function, and strength. α-Actinin has an actin binding domain and a calmodulin homology domain separated by a long rod domain. Using molecular dynamics and normal mode analysis, we suggest that the α-actinin rod domain has flexible terminal regions which can twist and extend under mechanical stress, yet has a highly rigid interior region stabilized by aromatic packing within each spectrin repeat, by electrostatic interactions between the spectrin repeats, and by strong salt bridges between its two anti-parallel monomers. By exploring the natural vibrations of the α-actinin rod domain and by conducting bending molecular dynamics simulations we also predict that bending of the rod domain is possible with minimal force. We introduce computational methods for analyzing the torsional strain of molecules using rotating constraints. Molecular dynamics extension of the α-actinin rod is also performed, demonstrating transduction of the unfolding forces across salt bridges to the associated monomer of the α-actinin rod domain.

The cell interacts with its environment in both biochemical and mechanical ways. In this study we explore one of the ways in which the cell interacts mechanically with its environment. α-Actinin is a cytoskeletal crosslinker: it functions to scaffold the cytoskeletal actin filaments that provide mechanical reinforcement to the cell. In its functional environment α-actinin is exposed to a multitude of mechanical stresses as it attaches itself to a dynamic network of actin filaments. The actin filaments extend, rotate, and bend the α-actinin crosslinkers. In this study we employ molecular dynamics techniques to understand the structural characteristics of α-actinin that underlie its ability to provide a scaffold in such a stressed environment. We analyzed the natural frequencies of α-actinin and simulated force-induced bending, extension, and twisting. Our results suggest that α-actinin has structural flexibility facilitating crosslinking in a dynamic environment and also structural rigidity stabilizing the linkage in the stressed environment. We have discovered novel natural bending movements of the rod domain that enhance its function as a crosslinker. We have also demonstrated the specific structural characteristics of α-actinin that give it the previously suggested property of having partial flexibility. Our results enhance the understanding of structural mechanics in the cytoskeletal molecules.

Development of tau aggregation inhibitors for Alzheimer's disease

A variety of human diseases are suspected to be directly linked to protein misfolding. Highly organized protein aggregates, called amyloid fibrils, and aggregation intermediates are observed; these are considered to be mediators of cellular toxicity and thus attract a great deal of attention from investigators. Neurodegenerative pathologies such as Alzheimer's disease account for a major part of these protein misfolding diseases. The last decade has witnessed a renaissance of interest in inhibitors of tau aggregation as potential disease-modifying drugs for Alzheimer's disease and other "tauopathies". The recent report of a phase II clinical trial with the tau aggregation inhibitor MTC could hold promise for the validation of the concept. This Review summarizes the available data concerning small-molecule inhibitors of tau aggregation from a medicinal chemistry point of view.

Electrostatics-defying interaction between arginine termini as a thermodynamic driving force in protein-protein interaction

Apparent electrostatics-defying clustering of arginines attributed as screening effect of solvent is in this study examined as a possible thermodynamic driving force in protein-protein interaction. A dataset of 266 protein dimers is found to have approximately 22% arginines mutually paired and approximately 17% pairs in interaction across interfaces and thus putative "hotspots" of protein-protein interaction. The pairing, uncorrelated with inter or intramolecular context, could be contributing in protein folding as well, and, uncorrelated with solvent access, could be driven by effects that are generic to solvent and protein structures. Mutually stacked at shorter distances but in diverse geometrical modes otherwise, the cations tend to be in gross deficit of hydrogen-bond partners, and contributing electrostatics across protein-protein interface that, on average, is repulsive for protein-protein interaction. Embedded in local environment enriched in polarizable residues, aromatic, aliphatic, and anionic, the arginines may contribute to protein-protein interaction via environmental polarization response to electrostatics of cation clustering, a possible new principle in molecular recognition.

Persistence of birefringence in sheared solutions of wormlike micelles

When aqueous solutions containing wormlike micelles (worms) are sheared, the micellar chains tend to align with the flow, which in turn leads to flow-birefringence. When shear is stopped, the worms rapidly revert to an isotropic state in typical samples, and the birefringence disappears. In this study, we present a system of cationic worms that shows a different behavior: not only do the samples become intensely birefringent when sheared but the birefringence also persists for hours (and even days) after shear is stopped. These results suggest that shear-aligned worms in the sample are trapped in their aligned state for long periods of time, an aspect that is confirmed by cryo-transmission electron microscopy (cryo-TEM). We seek to determine the origin of this unusual behavior. Our results show that the persistent birefringence is observed for cationic worms induced by hydroxy-naphthoate but not salicylate counterions. These observations suggest that the micellar alignment is stabilized by intermicellar attractive interactions (such as pi-pi and cation-pi) that arise when large aromatic counterions are anchored within the micelles.

Trityl-derivatized carbohydrates immobilized on a polystyrene microplate

Carbohydrate biosensors, including carbohydrate arrays, are attracting increased attention for the comprehensive and high-throughput investigation of protein-carbohydrate interactions. Here, we describe an effective approach to fabricating a robust microplate-based carbohydrate array capable of probing protein binding and screening for inhibitors in a high-throughout manner. This approach involves the derivatization of carbohydrates with a trityl group through an alkyl linker and the immobilization of the trityl-derivatized carbohydrates (mannose and maltose) onto microplates noncovalently to construct carbohydrate arrays. The trityl carbohydrate derivative has very good immobilization efficiency for polystyrene microplates and strong resistance to aqueous washing. The carbohydrate arrays can probe the interactions with the lectin Concanavalin A and screen this protein for the well-known inhibitors methyl alpha-D-mannopyranoside and methyl alpha-D-glucopyranoside in a high-throughput manner. The method described in this paper represents a convenient way of fabricating robust noncovalent carbohydrate arrays on microplates and offers a convenient platform for high-throughput drug screening.

Mechanism and dynamics of translesion DNA synthesis catalyzed by the Escherichia coli Klenow fragment

Translesion DNA synthesis represents the ability of a DNA polymerase to incorporate and extend beyond damaged DNA. In this report, the mechanism and dynamics by which the Escherichia coli Klenow fragment performs translesion DNA synthesis during the misreplication of an abasic site were investigated using a series of natural and non-natural nucleotides. Like most other high-fidelity DNA polymerases, the Klenow fragment follows the "A-rule" of translesion DNA synthesis by preferentially incorporating dATP opposite the noninstructional lesion. However, several 5-substituted indolyl nucleotides lacking classical hydrogen-bonding groups are incorporated approximately 100-fold more efficiently than the natural nucleotide. In general, analogues that contain large substituent groups in conjunction with significant pi-electron density display the highest catalytic efficiencies ( k cat/ K m) for incorporation. While the measured K m values depend upon the size and pi-electron density of the incoming nucleotide, k cat values are surprisingly independent of both biophysical features. As expected, the efficiency by which these non-natural nucleotides are incorporated opposite templating nucleobases is significantly reduced. This reduction reflects minimal increases in K m values coupled with large decreases in k cat values. The kinetic data obtained with the Klenow fragment are compared to that of the high-fidelity bacteriophage T4 DNA polymerase and reveal distinct differences in the dynamics by which these non-natural nucleotides are incorporated opposite an abasic site. These biophysical differences argue against a unified mechanism of translesion DNA synthesis and suggest that polymerases employ different catalytic strategies during the misreplication of damaged DNA.

Through-space interactions between parallel-offset arenes at the van der Waals distance: 1,8-diarylbiphenylene syntheses, structure and QM computations

A model for studying polar-pi interactions between arenes spaced at van der Waals distances is developed on the basis of peri-diarylbiphenylenes. A set of 1,8-diarylbiphenylenes is synthesized comprising two Hammett series, one with reference to mesityl ring interactions and the other with reference to pentafluorophenyl ring interactions. X-Ray crystal structures of several derivatives are determined. Barriers to rotation of the probe aryl ring are derived from dynamic NMR data and show a trend for the mesityl reference series (DeltaG(not equal) vs. sigma(0)). The model is also used as a test for comparison of modern density functional methods, including B3LYP, M06-2X and BMK functionals; dispersive effects are seen to be an important factor in the proper theoretical treatment of arene interactions.

Design, synthesis, and biological evaluation of glycine-based molecular tongs as inhibitors of Abeta1-40 aggregation in vitro

A series of N-terminus benzamides of glycine-based symmetric peptides, linked to m-xylylenediamine and 3,4'-oxydianiline spacers, were prepared and tested as inhibitors of beta-amyloid peptide Abeta(1-40) aggregation in vitro. Compounds with good anti-aggregating activity were detected. Polyphenolic amides showed the highest anti-aggregating activity, with IC(50) values in the micromolar range. Structure-activity relationships suggested that pi-pi stacking and hydrogen-bonding interactions play a key role in the inhibition of Abeta(1-40) self-assembly leading to amyloid fibrils.

Structural elements regulating amyloidogenesis: a cholinesterase model system

Polymerization into amyloid fibrils is a crucial step in the pathogenesis of neurodegenerative syndromes. Amyloid assembly is governed by properties of the sequence backbone and specific side-chain interactions, since fibrils from unrelated sequences possess similar structures and morphologies. Therefore, characterization of the structural determinants driving amyloid aggregation is of fundamental importance. We investigated the forces involved in the amyloid assembly of a model peptide derived from the oligomerization domain of acetylcholinesterase (AChE), AChE_586-599, through the effect of single point mutations on β-sheet propensity, conformation, fibrilization, surfactant activity, oligomerization and fibril morphology. AChE_586-599 was chosen due to its fibrilization tractability and AChE involvement in Alzheimer's disease. The results revealed how specific regions and residues can control AChE_586-599 assembly. Hydrophobic and/or aromatic residues were crucial for maintaining a high β-strand propensity, for the conformational transition to β-sheet, and for the first stage of aggregation. We also demonstrated that positively charged side-chains might be involved in electrostatic interactions, which could control the transition to β-sheet, the oligomerization and assembly stability. Further interactions were also found to participate in the assembly. We showed that some residues were important for AChE_586-599 surfactant activity and that amyloid assembly might preferentially occur at an air-water interface. Consistently with the experimental observations and assembly models for other amyloid systems, we propose a model for AChE_586-599 assembly in which a steric-zipper formed through specific interactions (hydrophobic, electrostatic, cation-π, SH-aromatic, metal chelation and polar-polar) would maintain the β-sheets together. We also propose that the stacking between the strands in the β-sheets along the fiber axis could be stabilized through π-π interactions and metal chelation. The dissection of the specific molecular recognition driving AChE_586-599 amyloid assembly has provided further knowledge on such poorly understood and complicated process, which could be applied to protein folding and the targeting of amyloid diseases.

Modulation of the enzymatic efficiency of ferredoxin-NADP(H) reductase by the amino acid volume around the catalytic site

Ferredoxin (flavodoxin)-NADP(H) reductases (FNRs) are ubiquitous flavoenzymes that deliver NADPH or low-potential one-electron donors (ferredoxin, flavodoxin, adrenodoxin) to redox-based metabolic reactions in plastids, mitochondria and bacteria. Plastidic FNRs are quite efficient reductases. In contrast, FNRs from organisms possessing a heterotrophic metabolism or anoxygenic photosynthesis display turnover numbers 20- to 100-fold lower than those of their plastidic and cyanobacterial counterparts. Several structural features of these enzymes have yet to be explained. The residue Y308 in pea FNR is stacked nearly parallel to the re-face of the flavin and is highly conserved amongst members of the family. By computing the relative free energy for the lumiflavin-phenol pair at different angles with the relative position found for Y308 in pea FNR, it can be concluded that this amino acid is constrained against the isoalloxazine. This effect is probably caused by amino acids C266 and L268, which face the other side of this tyrosine. Simple and double FNR mutants of these amino acids were obtained and characterized. It was observed that a decrease or increase in the amino acid volume resulted in a decrease in the catalytic efficiency of the enzyme without altering the protein structure. Our results provide experimental evidence that the volume of these amino acids participates in the fine-tuning of the catalytic efficiency of the enzyme.

Tuning peptoid secondary structure with pentafluoroaromatic functionality: a new design paradigm for the construction of discretely folded peptoid structures

Peptoids, or oligomers of N-substituted glycine, are an important class of non-native polymers whose close structural similarity to natural alpha-peptides and ease of synthesis offer significant advantages for the study of biomolecular interactions and the development of biomimetics. Peptoids that are N-substituted with alpha-chiral aromatic side chains have been shown to adopt either helical or "threaded loop" conformations, depending upon solvent and oligomer length. Elucidation of the factors that impact peptoid conformation is essential for the development of general rules for the design of peptoids with discrete and novel structures. Here, we report the first study of the effects of pentafluoroaromatic functionality on the conformational profiles of peptoids. This work was enabled by the synthesis of a new, alpha-chiral amine building block, (S)-1-(pentafluorophenyl)ethylamine (S-2), which was found to be highly compatible with peptoid synthesis (delivering (S)-N-(1-(pentafluorophenyl)ethyl)glycine oligomers). The incorporation of this fluorinated monomer unit allowed us to probe both the potential for pi-stacking interactions along the faces of peptoid helices and the role of side chain electrostatics in peptoid folding. A series of homo- and heteropeptoids derived from S-2 and non-fluorinated, alpha-chiral aromatic amide side chains were synthesized and characterized by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. Enhancement of pi-stacking by quadrupolar interactions did not appear to play a significant role in stabilizing the conformations of heteropeptoids with alternating fluorinated and non-fluorinated side chains. However, incorporation of (S)-N-(1-(pentafluorophenyl)ethyl)glycine monomers enforced helicity in peptoids that typically exhibit threaded loop conformations. Moreover, we found that the incorporation of a single (S)-N-(1-(pentafluorophenyl)ethyl)glycine monomer could be used to selectively promote looped or helical structure in this important peptoid class by tuning the electronics of nearby heteroatoms. The strategic installation of this monomer unit represents a new approach for the manipulation of canonical peptoid structure and the construction of novel peptoid architectures.

Tunable columnar mesophases utilizing C2 symmetric aromatic donor-acceptor complexes

Derivatives of relatively electron rich 1,5-dialkoxynaphthalene (Dan) donors and relatively electron deficient 1,4,5,8-naphthalenetetracarboxylic diimide (Ndi) acceptors have been exploited in the folding and self-assembly of a variety of complex molecular systems in solution. Here, we report the use of Dan and Ndi derivatives to direct assembly of extended columns with alternating face-centered stacked structure in the solid state. A variety of 1:1 Dan:Ndi mixtures produced mesophases that were found to be stable over temperature ranges extending up to 110 degrees C. Analysis of these mesophases indicates mixtures with soft/plastic crystal phases and a few mixtures with the thermodynamic properties of true liquid crystals, all composed of alternating donor-acceptor columns within. Importantly, a correspondence was found between the clearing and crystallization points of the mesophase mixtures and the melting/clearing points of the component Ndi and Dan units, respectively. This correspondence enables the predictable tuning of mesophase phase transition temperatures. The study of sterically hindered derivatives led to a set of mixtures in which a dramatic and sudden color change (deep red to yellow) was observed upon crystallization of the mesophase due to a phase separation of the component donor and acceptor units.

Substituent effects in C6F6-C6H5X stacking interactions

Parallel displaced and sandwich configurations of hexafluorobenzene-substituted benzene dimers are studied by ab initio molecular orbital methods up to the MP2(full)/aug-cc-pVDZ level of theory to reveal how substituents influence pi-pi interactions. Two minimum energy configurations are found, one with the substituent group away from the pi-face of the hexafluorobenzene ring (2a-f) and the other with the substituent group on top of the pi-face of the hexafluorobenzene (3a-f). Higher binding energies are predicted for dimers with the substituent on the pi-face (3a-f). All sandwich dimers (4a-e) are found to be saddle points on the potential energy surfaces. A parallel-displaced minimum energy configuration is also predicted for the parent complex, C6F6-C6H6, which is in contrast to predictions based on quadrupole moments of benzene and hexafuorobenzene. The preference for the parallel displaced, rather than the sandwich configuration, is rationalized based on the smaller interplanar distance in the former. The closeness of contact in the parallel-displaced dimers leads to greater binding energies. The shape of the electron density isosurface of the monomers is suggested to provide a guide for the prediction of how arenes stack with one another. A large difference in binding energy between the C6F6 complex of aniline (3e) and N,N-dimethylaniline (3f) is calculated, and charge-transfer interactions are suggested to play a role in the latter.

Stabilization of the Catalytic Thiolate in a Mammalian Glutaredoxin: Structure, Dynamics and Electrostatics of Reduced Pig Glutaredoxin and its Mutants

The variety of functions performed by proteins of the thioredoxin superfamily, including glutaredoxins, involves the wide range of redox potential associated with the -Cys-X-X-Cys- motif found in their active sites. The determinants of these differences in redox potential are still obscure. A better understanding requires a detailed characterization of the reduced state of these enzymes, especially because the lowered pK(a) of the reduced N-terminal active-site cysteine is a key feature of these enzymes' chemistry, including their redox potential. Analysis of the factors controlling this pK(a) is complicated by the apparent structural heterogeneity of the reduced active sites across glutaredoxins. In this family, pig glutaredoxin (pGrx) was one of the first to be functionally characterized, including some intriguing mutagenesis data, but a structure of its reduced state has been lacking. We used long molecular dynamics simulations and electrostatic calculations to analyze the structure, dynamics and electrostatics of reduced pGrx and some of its mutants. Comparison with experimental data is drawn whenever possible. It is shown that a dynamic model is essential to capture the structural properties of the cationic side-chains around the -Cys22-Pro23-Phe24-Cys25- sequence in the pGrx active site. Examples include Arg26, which can swing to stack on this sequence, and Lys19 which can contact the thiolate. However, contrary to a commonly held hypothesis, these cationic side-chains provide little stabilization for the thiolate, implying that they affect the enzymatic activity via other mechanisms. The pK(a) value of nucleophilic cysteine 22 (pK(a)(22)) is dominated by local hydrogen-bonds, formed only in a well-defined active-site conformation, supported by a comparison between the calculated and experimental values of pK(a)(22). The edge of the aromatic ring of Phe24 is polar enough to contribute to stabilize the thiolate, consistent with the conserved aromatic side-chain at this position in the glutaredoxin motif. The locality and directionality of the hydrogen bonds in the active site suffice to explain the vast difference between the pK(a) values of its two cysteine residues. A control of the cysteine pK(a) values by local hydrogen bonds implies that the peripheral ionized side-chains can evolve independently of the maintenance of these pK(a) values, maybe guided instead by substrate recognition. Comparison with other glutaredoxins indicates that the calculated pK(a) values of the N-terminal cysteine are better conserved than those of the C-terminal cysteine. Overall, a methodological strategy to systematically compare all reduced enzymes of this family emerges.

Oxoanion Binding by Flexible Guanidiniocarbonyl Pyrrole−Ammonium Bis-Cations in Water

The syntheses of several bis-cations 1-5 with a simple primary ammonium cation attached via flexible linkers of varying length to a guanidiniocarbonyl pyrrole oxo anion binding site are reported. In UV-binding studies in aqueous buffer solution these bis-cations showed efficient binding of various N-acetyl amino acid carboxylates. However, complex affinity is significantly depending on both the anion and the length of the linker in the bis-cation. With increasing linker length, complex stability first increases until an optimum is reached for bis-cation 3 with a C4-linker. Then the complex stability decreases again. The best binding substrate in this series is N-acetyl phenyl alanine, most likely due to additional cation-pi-interactions between the aromatic ring and the guanidiniocarbonyl pyrrole cation. The formation of the complex between bis-cation 3 and N-acetyl phenyl alanine carboxylate was investigated further by fluorescence titrations and NOE studies, as well as molecular mechanics calculations.

Direct measurements of the interaction between pyrene and graphite in aqueous media by single molecule force spectroscopy: understanding the pi-pi interactions

Pyrene derivatives can absorb onto the surface of carbon nanotubes and graphite particles through pi-pi interactions to functionalize these inorganic building blocks with organic surface moieties. Using single molecule force spectroscopy, we have demonstrated the first direct measurement of the interaction between pyrene and a graphite surface. In particular, we have connected a pyrene molecule onto an AFM tip via a flexible poly(ethylene glycol) (PEG) chain to ensure the formation of a molecular bridge. The pi-pi interaction between pyrene and graphite is thus indicated to be approximately 55 pN with no hysteresis between the desorption and adhesion forces.

Geometry of nonbonded interactions involving planar groups in proteins

Although hydrophobic interaction is the main contributing factor to the stability of the protein fold, the specificity of the folding process depends on many directional interactions. An analysis has been carried out on the geometry of interaction between planar moieties of ten side chains (Phe, Tyr, Trp, His, Arg, Pro, Asp, Glu, Asn and Gln), the aromatic residues and the sulfide planes (of Met and cystine), and the aromatic residues and the peptide planes within the protein tertiary structures available in the Protein Data Bank. The occurrence of hydrogen bonds and other nonconventional interactions such as C-H...pi, C-H...O, electrophile-nucleophile interactions involving the planar moieties has been elucidated. The specific nature of the interactions constraints many of the residue pairs to occur with a fixed sequence difference, maintaining a sequential order, when located in secondary structural elements, such as alpha-helices and beta-turns. The importance of many of these interactions (for example, aromatic residues interacting with Pro or cystine sulfur atom) is revealed by the higher degree of conservation observed for them in protein structures and binding regions. The planar residues are well represented in the active sites, and the geometry of their interactions does not deviate from the general distribution. The geometrical relationship between interacting residues provides valuable insights into the process of protein folding and would be useful for the design of protein molecules and modulation of their binding properties.

Conformational analysis of endomorphin-2 analogs with phenylalanine mimics by NMR and molecular modeling

We investigated a series of conformations of endomorphin-2 (EM-2) analogs substituted by phenylglycine (Phg) and homophenylalanine (Hfe) in the position 3 or 4 by two-dimensional (1)H NMR spectroscopy and molecular modeling. Evaluating the aromatic interactions and the dihedral angles in these phenylalanine mimics, we have observed that the conformations in trans isomer have varied from extended to folded as bioactivity decreases. It is suggested that the flexibility of aromatic side chain affects the backbone of EM-2 to adopt folded structures, which may block the ligands in binding to micro-opioid receptor.

Chiral recognition mass spectrometry: remarkable effects observed from the relative ion abundances of ternary diastereomeric complexes using electrospray ionization

The relative abundances of ternary diastereomeric complexes (composed each from a cinchonane-type chiral selector, a model chiral acid, and an alkali cation) are shown to change remarkably and fortuitously with variation in concentration and type of alkali metal using electrospray ionization-mass spectrometry and competitive binding analysis.

Proton-coupled electron transfer in a biomimetic peptide as a model of enzyme regulatory mechanisms

Proton-coupled electron-transfer reactions are central to enzymatic mechanism in many proteins. In several enzymes, essential electron-transfer reactions involve oxidation and reduction of tyrosine side chains. For these redox-active tyrosines, proton transfer couples with electron transfer, because the phenolic pKA of the tyrosine is altered by changes in the tyrosine redox state. To develop an experimentally tractable peptide system in which the effect of proton and electron coupling can be investigated, we have designed a novel amino acid sequence that contains one tyrosine residue. The tyrosine can be oxidized by ultraviolet photolysis or electrochemical methods and has a potential cross-strand interaction with a histidine residue. NMR spectroscopy shows that the peptide forms a beta-hairpin with several interstrand dipolar contacts between the histidine and tyrosine side chains. The effect of the cross-strand interaction was probed by electron paramagnetic resonance and electrochemistry. The data are consistent with an increase in histidine pKA when the tyrosine is oxidized; the effect of this thermodynamic coupling is to increase tyrosyl radical yield at low pH. The coupling mechanism is attributed to an interstrand pi-cation interaction, which stabilizes the tyrosyl radical. A similar interaction between histidine and tyrosine in enzymes provides a regulatory mechanism for enzymatic electron-transfer reactions.

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.

Parametrization of 1-Butyl-3-methylimidazolium Hexafluorophosphate/Nitrate Ionic Liquid for the GROMOS Force Field

A united-atom model of 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF(6)]) and 1-butyl-3-methylimidazolium nitrate ([BMIM][NO(3)]) is developed in the framework of the GROMOS96 43A1(1) force field. These two ionic liquids are parametrized, and their equilibrium properties in the 298-363 K temperature range are subjected to validation against known experimental properties, namely, density, self-diffusion, shear viscosity, and isothermal compressibility. The ionic radial/spatial distributions, pi interaction, gauche/trans populations of the butyl tail, and enthalpies of vaporization are also reported. The properties obtained from the molecular dynamics simulations agree with experimental data and have the same temperature dependence. The strengths and weakness of our model are discussed.

Effects of i and i+3 residue identity on cis-trans isomerism of the aromatic(i+1)-prolyl(i+2) amide bond: implications for type VI beta-turn formation

Cis-trans isomerization of amide bonds plays critical roles in protein molecular recognition, protein folding, protein misfolding, and disease. Aromatic-proline sequences are particularly prone to exhibit cis amide bonds. The roles of residues adjacent to a tyrosine-proline residue pair on cis-trans isomerism were examined. A short series of peptides XYPZ was synthesized and cis-trans isomerism was analyzed. Based on these initial studies, a series of peptides XYPN, X = all 20 canonical amino acids, was synthesized and analyzed by NMR for i residue effects on cis-trans isomerization. The following effects were observed: (a) aromatic residues immediately preceding Tyr-Pro disfavor cis amide bonds, with K(trans/cis)= 5.7-8.0, W > Y > F; (b) proline residues preceding Tyr-Pro lead to multiple species, exhibiting cis-trans isomerization of either or both X-Pro amide bonds; and (c) other residues exhibit similar values of K(trans/cis) (= 2.9-4.2), with Thr and protonated His exhibiting the highest fraction cis. beta-Branched and short polar residues were somewhat more favorable in stabilizing the cis conformation. Phosphorylation of serine at the i position modestly increases the stability of the cis conformer. In addition, the effect of the i+3 residue was examined in a limited series of peptides TYPZ. NMR data indicated that aromatic residues, Pro, Asn, Ala, and Val at the i+3 residue all favor cis amide bonds, with aromatic residues and Asn favoring more compact phi at Tyr(cis) and Ala and Pro favoring more extended phi at Tyr(cis). D-Alanine at the i+3 position particularly disfavors cis amide bonds.

Substituent Effects Control the Self-Association of Molecular Clips in the Crystalline State

We report the X-ray crystal structure of 11 molecular clips and analyze the influence of substituents (e.g., OMe, Me, and NO2) and their location on the observed crystal packing. Molecular clips 3a and 3b form tapelike structures in the crystal due to pi-pi interactions between the aromatic walls. Compounds 3d, 3eC, and 3fC form dimers driven by critical C-H...O interactions and then form tapes driven by pi-pi interactions in the crystal. These two building motifs, pi-pi and C-H...O interactions, can be used to rationalize the enantio- and diastereoselectivity observed in the X-ray crystal structures of the remaining five molecular clips. For example, the C-H...O interactions are found to dictate the formation of homochiral dimers in the structures of (+/-)-3eT and (+/-)-3fT and to control the diastereoselective formation of 6a2-6c2 dimeric motifs with internal p-dimethoxy-o-xylylene walls. Overall, the results suggest that substituent effects that induce even weak intermolecular interactions (e.g., C-H...O) can be used to reliably control crystal packing within glycoluril-based systems.

Characterisation of stationary phases in subcritical fluid chromatography with the solvation parameter model IV

The purpose of the present work was to systematically study the chromatographic behaviour of different aromatic stationary phases in a subcritical fluid mobile phase. We attempted to assess the chemical origin of the differences in retention characteristics between the different columns. Various types of aromatic stationary phases, all commercially available, were investigated. The effect of the nature of the aromatic bonding on interactions between solute and stationary phases and between solute and carbon dioxide-methanol mobile phase was studied by the use of a linear solvation energy relationship (LSER): the solvation parameter model. This study was performed to provide a greater knowledge of the properties of these phases in subcritical fluid chromatography, and to allow a more rapid and efficient choice of aromatic stationary phase in regard of the chemical nature of the solutes to be separated. Charge transfer interactions naturally contribute to the retention on all these stationary phases but are completed by various other types of interactions, depending on the nature of the aromatic group. The solvation vectors were used to compare the different phase properties. In particular, the similarities in the chromatographic behaviour of porous graphitic carbon (PGC), polystyrene-divinylbenzene (PS-DVB) and aromatic-bonded silica stationary phases are evidenced.

NMR analysis of aromatic interactions in designed peptide beta-hairpins

Designed octapeptide beta-hairpins containing a central (D)Pro-Gly segment have been used as a scaffold to place the aromatic residues Tyr and Trp at various positions on the antiparallel beta-strands. Using a set of five peptide hairpins, aromatic interactions have been probed across antiparallel beta-sheets, in the non-hydrogen bonding position (Ac-L-Y-V-(D)P-G-L-Y/W-V-OMe: peptides 1 and 2), diagonally across the strands (Boc-Y/W-L-V-(D)P-G-W-L-V-OMe: peptides 3 and 6), and along the strands at positions i and i + 2 (Boc-L-L-V-(D)P-G-Y-L-W-OMe: peptide 4). Two peptides served as controls (Boc-L-L-V-(D)P-G-Y-W-V-OMe: peptide 5; Boc-L-Y-V-(D)P-G-L-L-V-OMe: peptide 7) for aromatic interactions. All studies have been carried out using solution NMR methods in CDCl(3) + 10% DMSO-d(6) and have been additionally examined in CD(3)OH for peptides 1 and 2. Inter-ring proton-proton nuclear Overhauser effects (NOEs) and upfield shifted aromatic proton resonances have provided firm evidence for specific aromatic interactions. Calculated NMR structures for peptides 1 and 2, containing aromatic pairs at facing non-hydrogen bonded positions, revealed that T-shaped arrangements of the interacting pairs of rings are favored, with ring current effects leading to extremely upfield chemical shifts and temperature dependences for specific aromatic protons. Anomalous far-UV CD spectra appeared to be a characteristic feature in peptides where the two aromatic residues are spatially proximal. The observation of the close approach of aromatic rings in organic solvents suggests that interactions of an electrostatic nature may be favored. This situation may be compared to the case of aqueous solutions, where clustering of aromatic residues is driven by solvophobic (hydrophobic) forces.