Showing papers on "Cooperativity published in 2009"
625 citations
TL;DR: This review describes some of the most characteristic features of the IDP conformational behavior and the unique response of IDPs to changes in their environment.
Abstract: Intrinsically disordered proteins (IDPs) differ from “normal” ordered proteins at several levels, structural, functional and conformational. Amino acid biases characteristic for IDPs determine their structural variability and lack of rigid well-folded structure. This structural plasticity is necessary for the unique functional repertoire of IDPs, which is complementary to the catalytic activities of ordered proteins. Amino acid biases also drive atypical responses of IDPs to changes in their environment. The conformational behavior of IDPs is characterized by the low cooperativity (or the complete lack thereof) of the denaturant-induced unfolding, lack of the measurable excess heat absorption peak(s) characteristic for the melting of ordered proteins, “turned out” response to heat and changes in pH, the ability to gain structure in the presence of various counter ions, osmolytes, membranes and binding partners, and by the unique response to macromolecular crowding. This review describes some of the most characteristic features of the IDP conformational behavior and the unique response of IDPs to changes in their environment.
312 citations
TL;DR: A novel electrochemical sensor was developed for sensitive and selective detection of mercury(II), based on thymine-Hg2+-thymine (T- Hg2-T) coordination chemistry, which afforded exquisite selectivity for H g2+ against a reservoir of other environmentally related metal ions, compared to existing anodic stripping voltammetry (ASV) techniques.
Abstract: A novel electrochemical sensor was developed for sensitive and selective detection of mercury(II), based on thymine−Hg2+−thymine (T−Hg2+−T) coordination chemistry. This strategy exploited the cooperativity of proximate poly-T oligonucleotides in coordination with Hg2+. Ferrocene (Fc)-tagged poly-T oligonucleotides were immobilized on the electrode surface via self-assembly of the terminal thiol moiety. In the presence of Hg2+, a pair of poly-T oligonucleotides could cooperatively coordinate with Hg2+, which triggered a conformational reorganization of the poly-T oligonucleotides from flexible single strands to relatively rigid duplexlike complexes, thus drawing the Fc tags away from the electrode with a substantially decreased redox current. The response characteristics of the sensor were thoroughly investigated using capillary electrophoresis and electrochemical measurements. The results revealed that the sensor showed a sensitive response to Hg2+ in a concentration range from 1.0 nM to 2.0 μM, with a de...
247 citations
TL;DR: It is demonstrated how integrins themselves could function as sensory molecules that begin sensing matrix properties even before large multi-molecular adhesion complexes are assembled.
Abstract: Integrins have emerged as key sensory molecules that translate chemical and physical cues from the extracellular matrix (ECM) into biochemical signals that regulate cell behavior. Integrins function by clustering into adhesion plaques, but the molecular mechanisms that drive integrin clustering in response to interaction with the ECM remain unclear. To explore how deformations in the cell-ECM interface influence integrin clustering, we developed a spatial-temporal simulation that integrates the micro-mechanics of the cell, glycocalyx, and ECM with a simple chemical model of integrin activation and ligand interaction. Due to mechanical coupling, we find that integrin-ligand interactions are highly cooperative, and this cooperativity is sufficient to drive integrin clustering even in the absence of cytoskeletal crosslinking or homotypic integrin-integrin interactions. The glycocalyx largely mediates this cooperativity and hence may be a key regulator of integrin function. Remarkably, integrin clustering in the model is naturally responsive to the chemical and physical properties of the ECM, including ligand density, matrix rigidity, and the chemical affinity of ligand for receptor. Consistent with experimental observations, we find that integrin clustering is robust on rigid substrates with high ligand density, but is impaired on substrates that are highly compliant or have low ligand density. We thus demonstrate how integrins themselves could function as sensory molecules that begin sensing matrix properties even before large multi-molecular adhesion complexes are assembled.
240 citations
TL;DR: This review summarizes studies of ErbB receptor extracellular regions in solution and of intact receptors at the cell surface, and attempts to reconcile the differences suggested by the two approaches.
220 citations
TL;DR: Single-molecule structural and functional assays are used to demonstrate directly that cadherin monomers interact via their N-terminal EC1 domain to form trans adhesive complexes and found that increasing the density of cadher in monomers cooperatively increased the probability of trans adhesive binding.
Abstract: The cadherin family of Ca2+-dependent cell adhesion proteins are critical for the morphogenesis and functional organization of tissues in multicellular organisms, but the molecular interactions between cadherins that are at the core of cell–cell adhesion are a matter of considerable debate. A widely-accepted model is that cadherins adhere in 3 stages. First, the functional unit of cadherin adhesion is a cis dimer formed by the binding of the extracellular regions of 2 cadherins on the same cell surface. Second, formation of low-affinity trans interactions between cadherin cis dimers on opposing cell surfaces initiates cell–cell adhesion. Third, lateral clustering of cadherins cooperatively strengthens intercellular adhesion. Evidence of these cadherin binding states during adhesion is, however, contradictory, and evidence for cooperativity is lacking. We used single-molecule structural (fluorescence resonance energy transfer) and functional (atomic force microscopy) assays to demonstrate directly that cadherin monomers interact via their N-terminal EC1 domain to form trans adhesive complexes. We could not detect the formation of cadherin cis dimers, but found that increasing the density of cadherin monomers cooperatively increased the probability of trans adhesive binding.
182 citations
TL;DR: The general binding polynomial formalism is described and specific theoretical and experimental examples of its application to isothermal titration calorimetry are provided.
Abstract: The theory of the binding polynomial constitutes a very powerful formalism by which many experimental biological systems involving ligand binding can be analyzed under a unified framework. The analysis of isothermal titration calorimetry (ITC) data for systems possessing more than one binding site has been cumbersome because it required the user to develop a binding model to fit the data. Furthermore, in many instances, different binding models give rise to identical binding isotherms, making it impossible to discriminate binding mechanisms using binding data alone. One of the main advantages of the binding polynomials is that experimental data can be analyzed by employing a general model-free methodology that provides essential information about the system behavior (e.g., whether there exists binding cooperativity, whether the cooperativity is positive or negative, and the magnitude of the cooperative energy). Data analysis utilizing binding polynomials yields a set of binding association constants and enthalpy values that conserve their validity after the correct model has been determined. In fact, once the correct model is validated, the binding polynomial parameters can be immediately translated into the model specific constants. In this chapter, we describe the general binding polynomial formalism and provide specific theoretical and experimental examples of its application to isothermal titration calorimetry.
152 citations
TL;DR: Isothermal titration calorimetry has broad scope in the analysis of cooperativity as it determines binding stiochiometries, affinities and thermodynamic parameters, including enthalpy and entropy in a single experiment.
Abstract: Cooperative binding pervades Nature This review discusses the use of isothermal titration calorimetry (ITC) in the identification and characterisation of cooperativity in biological interactions ITC has broad scope in the analysis of cooperativity as it determines binding stiochiometries, affinities and thermodynamic parameters, including enthalpy and entropy in a single experiment Examples from the literature are used to demonstrate the applicability of ITC in the characterisation of cooperative systems
129 citations
TL;DR: In this article, the acid-base cooperativity of SBA-15 mesoporous silicas co-condensed with aminopropyl groups as well as silica co-conditioned with dihydroimidazole groups was investigated.
123 citations
TL;DR: Kinetics showed strong positive cooperativity, which is consistent with the rotating catalysis model of this trimeric pump, and for the very hydrophilic cefazolin there was little sign of efflux, compared with other compounds that showed lower affinity to the pump.
Abstract: Multidrug efflux transporters, especially those that belong to the resistance-nodulation-division (RND) family, often show very broad substrate specificity and play a major role both in the intrinsic antibiotic resistance and, with increased levels of expression, in the elevated resistance of Gram-negative bacteria. However, it has not been possible to determine the kinetic behavior of these important pumps so far. This is partly because these pumps form a tripartite complex traversing both the cytoplasmic and outer membranes, with an outer membrane channel and a periplasmic adaptor protein, and it is uncertain if the behavior of an isolated component protein reflects that of the protein in this multiprotein complex. Here we use intact cells of Escherichia coli containing the intact multiprotein complex AcrB-AcrA-TolC, and measure the kinetic constants for various cephalosporins, by assessing the periplasmic concentration of the drug from their rate of hydrolysis by periplasmic β-lactamase and the rate of efflux as the difference between the influx rate and the hydrolysis rate. Nitrocefin efflux showed a Km of about 5 μM with little sign of cooperativity. For other compounds (cephalothin, cefamandole, and cephaloridine) that showed lower affinity to the pump, however, kinetics showed strong positive cooperativity, which is consistent with the rotating catalysis model of this trimeric pump. For the very hydrophilic cefazolin there was little sign of efflux.
123 citations
TL;DR: This work presents a model that allows a multitude of DBFs, each at different concentrations, to compete with one another for binding sites along the genome and produces an "occupancy profile," a probabilistic description of the DNA occupancy of each factor at each position.
Abstract: Hundreds of different factors adorn the eukaryotic genome, binding to it in large number. These DNA binding factors (DBFs) include nucleosomes, transcription factors (TFs), and other proteins and protein complexes, such as the origin recognition complex (ORC). DBFs compete with one another for binding along the genome, yet many current models of genome binding do not consider different types of DBFs together simultaneously. Additionally, binding is a stochastic process that results in a continuum of binding probabilities at any position along the genome, but many current models tend to consider positions as being either binding sites or not. Here, we present a model that allows a multitude of DBFs, each at different concentrations, to compete with one another for binding sites along the genome. The result is an "occupancy profile," a probabilistic description of the DNA occupancy of each factor at each position. We implement our model efficiently as the software package COMPETE. We demonstrate genome-wide and at specific loci how modeling nucleosome binding alters TF binding, and vice versa, and illustrate how factor concentration influences binding occupancy. Binding cooperativity between nearby TFs arises implicitly via mutual competition with nucleosomes. Our method applies not only to TFs, but also recapitulates known occupancy profiles of a well-studied replication origin with and without ORC binding. Importantly, the sequence preferences our model takes as input are derived from in vitro experiments. This ensures that the calculated occupancy profiles are the result of the forces of competition represented explicitly in our model and the inherent sequence affinities of the constituent DBFs.
TL;DR: It is shown that binding the activation domain of the mixed lineage leukemia (MLL) transcription factor to KIX induces a redistribution of the relative populations of KIX conformations toward a high-energy state in which the allosterically activated second binding site is already preformed, consistent with the Monod-Wyman-Changeux (WMC) model of allostery.
Abstract: Allosteric regulation is an effective mechanism of control in biological processes. In allosteric proteins a signal originating at one site in the molecule is communicated through the protein structure to trigger a specific response at a remote site. Using NMR relaxation dispersion techniques we directly observe the dynamic process through which the KIX domain of CREB binding protein communicates allosteric information between binding sites. KIX mediates cooperativity between pairs of transcription factors through binding to two distinct interaction surfaces in an allosteric manner. We show that binding the activation domain of the mixed lineage leukemia (MLL) transcription factor to KIX induces a redistribution of the relative populations of KIX conformations toward a high-energy state in which the allosterically activated second binding site is already preformed, consistent with the Monod−Wyman−Changeux (WMC) model of allostery. The structural rearrangement process that links the two conformers and by w...
TL;DR: In this paper, the authors present a systematic comparison of different polymers and effector classes that allow for the characterization of these contributions in chemomechanical polymers: they comprise ion pairing, metal coordination, stacking, cation-pi, dispersive, and hydrophobic forces.
Abstract: Molecular recognition is the basis for the operation of most biological functions; outside of nature, it has also been developed to a high degree of sophistication within the framework of supramolecular chemistry. More recently, selective noncovalent interactions, which constitute molecular recognition, are being used in intelligent new materials that transform chemical signals into actions, such as the release of drugs. The presence of supramolecular binding sites allows chemomechanical polymers to operate as sensors and actuators within a single unit without the need for any additional devices such as transducers or power supplies. A polymer can be designed so that a particular chemical substance, most often in aqueous surroundings, will trigger either a large expansion or a large contraction, depending on the mechanism. The translation of binding energy into mechanical motion can, with a suitable arrangement of the materials in tubes or on flexible films, be harnessed for unidirectional drives, flow control, the liberation of drugs, or the uptake of toxic compounds, among other applications. Miniaturization of the polymer particles allows one to enhance both the sensitivity and speed of the response, which is of particular importance in sensing. The basis for the selective response to external effector compounds, such as metal ions, amino acids, peptides, or nucleotides, is their noncovalent interaction with complementary functions covalently bound to the polymer network. With suitable polymers, selectivity between structural isomers, and even between enantiomers, as triggers can be achieved. As with supramolecular complexes in solution, the underlying interactions in polymers comprise a variety of noncovalent binding mechanisms, which are not easy to distinguish and quantify, and more so with polymers that are not monodisperse. In this Account, we present systematic comparisons of different polymers and effector classes that allow, for the first time, the characterization of these contributions in chemomechanical polymers: they comprise ion pairing, metal coordination, stacking, cation-pi, dispersive, and hydrophobic forces. In contrast, hydrogen bonding has a major role primarily in the hydrogel network structure itself. The fully reversible polymer volume changes are essentially determined by water uptake or release. In gels derived from boronic acid, glucose can serve as a cross-linking effector in promoting contractions via strong, reversible covalent bond formation in a highly distinctive manner. Cooperativity between two different effector compounds is more frequently seen with such polymers than in solution: it leads to logical AND gates by different motions of the particles, with a direct communication link to the outside world. For example, with a polymer that bears several recognition sites, triggering peptides induce motion only if Zn(2+) or Cu(2+) ions are simultaneously present. The molecular recognition mechanisms that cause volume changes in polymers share similarities with extensively studied supramolecular systems in solution, but there are also remarkable differences. In this Account, we bring the knowledge learned from solution studies to bear on our systematic analysis of polymeric systems in an effort to promote the effective harnessing of the forces involved in chemomechanical polymers and the smart materials that can be created with them.
TL;DR: It is argued that in classical in vitro experiments the lack of GTP makes ligand-binding properties dependent on the available pool of G protein, and this competition explains some in vivo effects of orphan GPCRs.
TL;DR: A combination of vibrational spectroscopy conducted under molecular beam conditions and quantum chemical calculation has established the intrinsic three-dimensional structures of the cellulose disaccharide and, focusing on the critical beta1,4-linkage at the nonreducing end of the growing cellulose polymer, its C-4' epimer.
Abstract: A combination of vibrational spectroscopy conducted under molecular beam conditions and quantum chemical calculation has established the intrinsic three-dimensional structures of the cellulose disaccharide and, focusing on the critical β1,4-linkage at the nonreducing end of the growing cellulose polymer, its C-4′ epimer. Left to their own devices they both adopt a cis (anti-ϕ/syn-ψ) glycosidic configuration, supported in the epimer by strong, cooperative inter-ring hydrogen bonding. In the cellulose disaccharide, however, where the OH-4′(Glc) group is equatorial, the cooperativity is reduced and the corresponding inter-ring hydrogen bonding is relatively weak. The cis conformational preference is still retained in their singly hydrated complexes. In the cellulose disaccharide insertion of the water molecule at the favored binding site between OH-4′ and the neighboring hydroxyl group OH-6′ promotes a structural reorganization to create a configuration that parallels that of its unhydrated epimer and greatl...
TL;DR: The results presented here point to the promise of MM-PBSA toward rationalizing molecular recognition at protein−protein interfaces, while establishing a general approach to handle explicit interfacial water molecules in such calculations.
Abstract: The calculation of protein interaction energetics is of fundamental interest, yet accurate quantities are difficult to obtain due to the complex and dynamic nature of protein interfaces. This is further complicated by the presence of water molecules, which can exhibit transient interactions of variable duration and strength with the protein surface. The T-cell receptor (TCR) and its staphylococcal enterotoxin 3 (SEC3) binding partner are well-characterized examples of a protein-protein interaction system exhibiting interfacial plasticity, cooperativity, and additivity among mutants. Specifically engineered mutants induce intercalating interfacial water molecules, which subsequently enhance protein-protein binding affinity. In this work, we perform a set of molecular mechanics (MM) Poisson-Boltzmann (PB) surface area (SA) calculations on the wild type and two mutant TCR-SEC3 systems and show that the method is able to discriminate between weak and strong binders only when key explicit water molecules are included in the analysis. The results presented here point to the promise of MM-PBSA toward rationalizing molecular recognition at protein-protein interfaces, while establishing a general approach to handle explicit interfacial water molecules in such calculations.
TL;DR: This review focuses on models in which the membranes are described as elastic sheets, and the receptors and ligands as anchored molecules, and finds that the thermal membrane roughness on the nanometre scale leads to a cooperative binding of anchored receptor and ligand molecules.
Abstract: Cell membranes interact via anchored receptor and ligand molecules. Central questions on cell adhesion concern the binding affinity of these membrane-anchored molecules, the mechanisms leading to the receptor–ligand domains observed during adhesion, and the role of cytoskeletal and other active processes. In this review, these questions are addressed from a theoretical perspective. We focus on models in which the membranes are described as elastic sheets, and the receptors and ligands as anchored molecules. In these models, the thermal membrane roughness on the nanometre scale leads to a cooperative binding of anchored receptor and ligand molecules, since the receptor–ligand binding smoothens out the membranes and facilitates the formation of additional bonds. Patterns of receptor domains observed in Monte Carlo simulations point towards a joint role of spontaneous and active processes in cell adhesion. The interactions mediated by the receptors and ligand molecules can be characterized by effective membrane adhesion potentials that depend on the concentrations and binding energies of the molecules.
TL;DR: It is shown that surprisingly, the opposite holds true when the double C2A/B-domain fragment of synaptotagmin-1 is used instead of isolated C2 domains, and when liposomes containing a physiological lipid composition are used.
Abstract: Neurotransmitter release is triggered by cooperative Ca2+-binding to the Ca2+-sensor protein synaptotagmin-1. Synaptotagmin-1 contains two C2 domains, referred to as the C2A and C2B domains, that bind Ca2+ with similar properties and affinities. However, Ca2+ binding to the C2A domain is not required for release, whereas Ca2+ binding to the C2B domain is essential for release. We now demonstrate that despite its expendability, Ca2+-binding to the C2A domain significantly contributes to the overall triggering of neurotransmitter release, and determines its Ca2+ cooperativity. Biochemically, Ca2+ induces more tight binding of the isolated C2A domain than of the isolated C2B domain to standard liposomes composed of phosphatidylcholine and phosphatidylserine. However, here we show that surprisingly, the opposite holds true when the double C2A/B-domain fragment of synaptotagmin-1 is used instead of isolated C2 domains, and when liposomes containing a physiological lipid composition are used. Under these conditions, Ca2+ binding to the C2B domain but not the C2A domain becomes the primary determinant of phospholipid binding. Thus, the unique requirement for Ca2+ binding to the C2B domain for synaptotagmin-1 in Ca2+-triggered neurotransmitter release may be accounted for, at least in part, by the unusual phospholipid-binding properties of its double C2A/B-domain fragment.
TL;DR: It is concluded that the thermodynamic coupling of the TetR domains caused by Tc binding and the resulting rigidification of the DNA-binding domains into a conformation that is incompatible with DNA binding are the fundamental factors leading to the allosteric response in TetR.
Abstract: Tetracycline (Tc) repressor (TetR) undergoes an allosteric transition upon interaction with the antibiotic, Tc, that abrogates its ability to specifically bind its operator DNA. In this work, by performing equilibrium protein unfolding experiments on wild-type TetR and mutants displaying altered allosteric responses, we have delineated a model to explain TetR allostery. In the absence of Tc, we show that the DNA-binding domains of this homodimeric protein are relatively flexible and unfold independently of the Tc binding/dimerization (TBD) domains. Once Tc is bound, however, the unfolding of the DNA binding domains becomes coupled to the TBD domains, leading to a large increase in DNA-binding domain stability. Noninducible TetR mutants display considerably less interdomain folding cooperativity upon binding to Tc. We conclude that the thermodynamic coupling of the TetR domains caused by Tc binding and the resulting rigidification of the DNA-binding domains into a conformation that is incompatible with DNA binding are the fundamental factors leading to the allosteric response in TetR. This allosteric mechanism can account for properties of the whole TetR family of repressors and may explain the functioning and evolution of other allosteric systems. Our model contrasts with the prevalent view that TetR populates two distinct conformations and that Tc causes a switch between these defined conformations.
TL;DR: It is proposed that the initial interaction of an antigen with a TCR may influence the conformation of oligomeric TCR complexes so that TCRs act cooperatively to transmit signals from peptide-MHC.
Abstract: The CD3epsilon subunit of the T cell receptor (TCR) complex undergoes a conformational change upon ligand binding that is thought to be important for the activation of T cells. To study this process, we built a molecular dynamics model of the transmission of the conformational change within the ectodomains of CD3. The model showed that the CD3 dimers underwent a stiffening effect that was funneled to the base of the CD3epsilon subunit. Mutation of two relevant amino acid residues blocked transmission of the conformational change and the differentiation and activation of T cells. Furthermore, this inhibition occurred even in the presence of excess endogenous CD3epsilon subunits. These results emphasize the importance of the conformational change in CD3epsilon for the activation of T cells and suggest the existence of unforeseen cooperativity between TCR complexes.
TL;DR: A general model of enzyme inhibition andactivation is introduced to allow one to interpret inhibition and activation from a mechanistic or physical perspective using the significance of cooperativity as a new approach.
Abstract: The rate of an enzymatic reaction may be changed by a moderator. Usually, the effect is to reduce the rate, and this is called inhibition. Sometimes the rate of enzyme reaction is raised, and this is called activation. Not only enzyme activation is subject of a less detailed presentation, but also enzyme inhibition and activation are very often discussed independently in enzymology. I attempt to introduce a general model of enzyme inhibition and activation to allow one to interpret inhibition and activation from a mechanistic or physical perspective using the significance of cooperativity as a new approach. The magnitude of interaction between substrate and inhibitor binding sites is given by the α parameter and the magnitude of increasing catalytic reaction constant is given by the β parameter, which both parameter values characterize the type of inhibition and activation. The moderation of mushroom tyrosinse is described by application of the model as a typical.
TL;DR: This review aims to summarize the current understanding of cooperativity in cytochromes P450, with a focus on the nature of cooperative effects in monomeric enzymes.
TL;DR: A new Calpha-side chain elastic network model of proteins that includes information about the physical identity of each residue and accurately accounts for the side-chain topology and packing within the structure is proposed and found that several substrate protein binding residues as well as sites related to ATPase activity belong to a single functional network in GroEL.
TL;DR: In naive, unphosphorylated EGF receptors, ligand binding is positively linked to receptor dimerization but the linkage is abolished upon autophosphorylation of the receptor.
TL;DR: The simulation model suggests that direct interactions between TFs are unlikely to be the main source of cooperativity between specific binding sites, because such interactions tend to lead to the formation of clusters on the DNA with undesirable side-effects.
TL;DR: It can be concluded that five of the Ca2+‐binding sites of TG2 influence its transglutaminase activity, two sites are involved in the regulation of GTP enzyme activity, and one determines antigenicity for autoantibodies in celiac patients.
Abstract: The multifunctional tissue transglutaminase 2 (TG2) has a four-domain structure with several Ca(2+)-regulated biochemical activities, including transglutamylation and GTP hydrolysis. The structure of the Ca(2+)-binding form of the human enzyme is not known, and its Ca(2+)-binding sites have not been fully characterized. By mutagenesis, we have targeted its active site Cys, three sites based on homology to Ca(2+)-binding residues of epidermal transglutaminase and factor XIIIa (S1-S3), and two regions with negative surface potentials (S4 and S5). CD spectroscopy, antibody-binding assay and GTPase activity measurements indicated that the amino acid substitutions did not cause major structural alterations. Calcium-45 equilibrium dialysis and isothermal calorimetric titration showed that both wild-type and active site-deleted enzymes (C277S) bind six Ca(2+). Each of the S1-S5 mutants binds fewer than six Ca(2+), S1 is a strong Ca(2+)-binding site, and mutation of one site resulted in the loss of more than one bound Ca(2+), suggesting cooperativity among sites. All mutants were deficient in transglutaminase activity, and GTP inhibited remnant activities. Like those of the wild-type enzyme, the GTPase activities of the mutants were inhibited by Ca(2+), except in the case of the S4 and S5 mutants, which exhibited increased activity. TG2 is the major autoantigen in celiac disease, and testing the reactivity of mutants with autoantibodies from celiac disease patients revealed that S4 strongly determines antigenicity. It can be concluded that five of the Ca(2+)-binding sites of TG2 influence its transglutaminase activity, two sites are involved in the regulation of GTPase activity, and one determines antigenicity for autoantibodies in celiac patients.
TL;DR: It is concluded that the formation of sequence-specific tertiary interactions in the Azoarcus ribo enzyme overlaps with neutralization of the phosphate charge, while tertiary folding of the Tetrahymena ribozyme requires additional counterions.
TL;DR: The interplay between two important non-covalent interactions involving aromatic rings (namely anion-pi and hydrogen bonding) is investigated and Bader's theory of atoms-in-molecules is used to characterize the interactions and analyze the strengthening or weakening of the interactions depending upon the variation of the charge density at the critical points.
Abstract: The interplay between two important non-covalent interactions involving aromatic rings (namely anion-pi and hydrogen bonding) is investigated. Very interesting cooperativity effects are present in complexes where anion-pi and hydrogen bonding interactions coexist. These effects are found in systems where the distance between the anion and the hydrogen-bond donor/acceptor molecule is as long as approximately 11 A. These effects are studied theoretically using the energetic and geometric features of the complexes, which were computed using ab initio calculations. We use and discuss several criteria to analyze the mutual influence of the non-covalent interactions studied herein. In addition we use Bader's theory of atoms-in-molecules to characterize the interactions and to analyze the strengthening or weakening of the interactions depending upon the variation of the charge density at the critical points.
TL;DR: This work estimates the length scale of molecular cooperativity xi for many glass-forming systems from the collective vibrations (the so-called boson peak) and demonstrates that xi directly correlates to the dependence of the structural relaxation on volume.
Abstract: The mechanism behind the steep slowing down of molecular motions upon approaching the glass transition remains a great puzzle Most of the theories relate this mechanism to the cooperativity in molecular motion In this work, we estimate the length scale of molecular cooperativity ξ for many glass-forming systems from the collective vibrations (the so-called boson peak) The obtained values agree well with the dynamic heterogeneity length scale estimated using four-dimensional NMR We demonstrate that ξ directly correlates to the dependence of the structural relaxation on volume This dependence presents only one part of the mechanism of slowing down the structural relaxation Our analysis reveals that another part, the purely thermal variation in the structural relaxation (at constant volume), does not have a direct correlation with molecular cooperativity These results call for a conceptually new approach to the analysis of the mechanism of the glass transition and to the role of molecular cooperativity