Effect of salt on the inter- and intramolecular hydrophobic interactions of macromolecules

The effect of salt on the structure of a low density lipoprotein (LDL) and on the reversible polymerization of bovine serum albumin (BSA) reduced with 2-mercaptoethanol was investigated by means of ultracentrifugal analysis. The chaotropic anion, e.g., SCN^– and I^–, at 5M completely disrupted the LDL structure and effectively dissociated BSA oligomers at lower concentrations. The parallelism between the anion order of these effects and that of the chaotropic effect suggested that the observed salt effects are primarily based on the disruption of hydrophobic interactions. The cation effectiveness disrupting the LDL structure followed the order of their promoting effect on the water structure, i.e., Li⁺>Na⁺>K⁺>Cs⁺. However, Cs⁺ was most effective in dissociating BSA oligomers, and this was attributed to the -complex formation with the aromatic amino acid side chains which otherwise contribute to the promotion of the intermolecular hydrophobic association.     

Luminescence on-off switching via reversible interconversion between inter- and intramolecular aurophilic interactions

Reversible interconversion between inter- and intramolecular AuAu interactions induces luminescence on/off switching in solid state. For the gold(I) photoluminescence system, intermolecular aurophilic interaction is a more significant factor than intramolecular aurophilic interaction.     

Comparison of inter- and intramolecular cyclodextrin complexes

Abstract

We present the first comparative steady-state and time-resolved fluorescence studies of inter- and intramolecular cyclodextrin complexes. Specifically, we report equilibrium and kinetic results for dansyl-glycine complexed with β-cyclodextrin (intermolecular) and the dansyl-glycine-β-cyclodextrin adduct (intramolecular). The fluorescence intensity decay profile for the intermolecular system is best described by a discrete triple exponential decay law. This is consistent with stepwise 1:1 and 2:1 (β-cyclodextrin:guest) inclusion complexation. Equilibrium constants are in line with previous results on similar species. In contrast, we found that the intramolecular case was described by a doubly exponential decay law—consistent with a single intramolecular inclusion complex. Displacement experiments, with borneol, confirm the simplicity of the intramolecular complex. In all cases, continuous distribution models failed to fit the experimental data.     

Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems

In several previous studies, we performed sensitivity analysis to gauge the relative importance of different atomic partial charges in determining protein-ligand binding. In this work, we gain further insights by decomposing these results into three contributions: desolvation, intramolecular interactions, and intermolecular interactions, again based on a Poisson continuum electrostatics model. Three protein kinase-inhibitor systems have been analyzed: CDK2-deschloroflavopiridol, PKA-PKI, and LCK-PP2. Although our results point out the importance of specific intermolecular interactions to the binding affinity, they also reveal the remarkable contributions from the solvent-mediated intramolecular interactions in some cases. Thus, it is necessary to look beyond analyzing protein-ligand interactions to understand protein-ligand recognition or to gain insights into designing ligands and proteins. In analyzing the contributions of the three components to the overall binding free energy, the PKA-PKI system with a much larger ligand was found to behave differently from the other two systems with smaller ligands. In the former case, the intermolecular interactions are very favorable, and together with the favorable solvent-mediated intramolecular interactions, they overcome the large desolvation penalties to give a favorable electrostatics contribution to the overall binding affinity. On the other hand, the other two systems with smaller ligands only present modest intermolecular interactions and they are not or are only barely sufficient to overcome the desolvation penalty even with the aid of the favorable intramolecular contributions. As a result, the binding affinity of these two systems do not or only barely benefit from electrostatics contributions.     

Carbocycles via enantioselective inter- and intramolecular iridium-catalysed allylic alkylations

Carbocycles with > 90% ee were prepared via Ir-catalysed asymmetric allylic alkylation/ring closing metathesis sequences or enantioselective Ir-catalysed intramolecular allylic alkylations.     

Reaction-phase-selective inter- and intramolecular photochemical reaction of 2-pyridone derivatives

Phase-selective photochemical reaction of 2-pyridone derivatives was examined. Irradiation of 1 in benzene mainly gave rearrangement products 2. However, intermolecular [4 + 4] photocycloaddition proceeded quantitatively in the solid state, affording photodimers 3. An effective pi-pi stacking and dipole-dipole interaction between two pyridone moieties might play important roles in an effective arrangement of 1 for photodimerization in their crystal structures. [reaction: see text]     

Mechanisms of inter- and intramolecular communication in GPCRs and G proteins

This study represents the first attempt to couple, by computational experiments, the mechanisms of intramolecular and intermolecular communication concerning a guanidine nucleotide exchange factor (GEF), the thromboxane A2 receptor (TXA2R), and the cognate G protein (Gq) in its heterotrimeric GDP-bound state. Two-way pathways mediate the communication between the receptor-G protein interface and both the agonist binding site of the receptor and the nucleotide binding site of the G protein. The increase in solvent accessibility in the neighborhoods of the highly conserved E/DRY receptor motif, in response to agonist binding, is instrumental in favoring the penetration of the C-terminus of Gqalpha in between the cytosolic ends of H3, H5, and H6. The arginine of the E/DRY motif is predicted to be an important mediator of the intramolecular and intermolecular communication involving the TXA2R. The receptor-G protein interface is predicted to involve multiple regions from the receptor and the G protein alpha-subunit. However, receptor contacts with the C-terminus of the alpha5-helix seem to be the major players in the receptor-catalyzed motion of the alpha-helical domain with respect to the Ras-like domain and in the formation of a nucleotide exit route in between the alphaF-helix and beta6/alpha5 loop of Gqalpha. The inferences from this study are of wide interest, as they are expected to apply to the whole rhodopsin family, given also the considerable G protein promiscuity.     

Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations

A protocol is described for the treatment of molecular polarization in force field calculations. The resulting model is consistent in that both inter- and intramolecular polarization are handled within a single scheme. An analytical formula for removing intramolecular polarization from a set of atomic multipoles for an arbitrary static structure or conformation is given. With the help of the intramolecular polarization, these permanent atomic multipoles can then be applied in modeling alternative conformations of a molecule. Equipped with this simple technique, one can derive transferable electrostatic parameters for peptides and proteins using flexible model compounds such as dipeptides. The proposed procedure is tested for its ability to describe the electrostatic potential around various configurations of the N-methylacetamide dimer. The effect of different intramolecular polarization schemes on the accuracy of a force field model of the electrostatic potential of alanine dipeptide is investigated. A group-based scheme for including direct intramolecular polarization is shown to be most successful in accounting for the conformational dependence of electrostatic potentials.     

A mild inter- and intramolecular amination of aryl halides with a combination of CuI and CsOAc

A unique combination of CuI and CsOAc was found to catalyze aryl amination under mild conditions. The reaction takes place at room temperature or at 90 °C with broad functional group compatibility. The intramolecular reaction was able to form five-, six-, and seven-membered rings with various protecting groups on the nitrogen atom. The scope of the intermolecular amination, as well as its applications to unsymmetrical N,N′-dialkylated phenylenediamines, was investigated.     

Dynamic equilibrium between a supramolecular capsule and bowl generated by inter- and intramolecular metal clipping

The metal-induced self-assembly of a resorcin[4]arene derivative 1 that has four pyridine units as pendent groups and two equivalents of [M(dppp)(OTf)(2)] (M=Pd, Pt) results in a dynamic equilibrium between an interclipped supramolecular capsule 3 and an intraclipped bowl 4 in nitromethane, although the interclipped capsule 3 is formed as a sole adduct in chloroform/methanol and the intraclipped bowl 4 is formed exclusively in an aqueous phase. This demonstrates how metal-induced self-assembly can be tuned by subtle changes in the solvent system. The coexistence of the two structures in nitromethane was characterized by NMR spectroscopy and coldspray ionization mass spectrometry (CSI-MS). The crystal structure of the interclipped capsule 3 b, which is composed of two units of ligand 1 and four Pt(II) ions, reveals the capsule cavity to have nanoscale dimensions of 15x20 A. NMR spectra show that the dynamic equilibrium between 3 and 4 is dependent on concentration and temperature. Temperature-dependent (1)H NMR spectroscopy was carried out from 273 to 343 K to verify the thermodynamic parameters that control the dynamic equilibrium process; the conversion from the interclipped supramolecular capsule 3 a to the intraclipped bowl 4 a is entropically favored and enthalpically disfavored. The rotational barrier of the restricted rotation of pyridine units in the intraclipped bowl 4 was determined by line-shape analysis.     

Contribution of inter- and intramolecular energy transfers to heat conduction in liquids

The molecular dynamics expression of heat flux, originally derived by Irving and Kirkwood [J. Chem. Phys. 18, 817 (1950)] for pairwise potentials, is generalized in this paper for systems with many-body potentials. The original formula consists of a kinetic part and a potential part, and the latter term is found in the present study to be expressible as a summation of contributions from all the many-body potentials defined in the system. The energy transfer among a set of sites for which a many-body potential is defined is discussed and evaluated by the rate of increase in the kinetic energy of each site due to the potential, and its accumulation over all the potentials in the system is shown to make up the potential part of the generalized expression. A molecular dynamics simulation for liquid n-octane was performed to demonstrate the applicability of the new expression obtained in this study to measure the heat flux and to elucidate the contributions of inter- and intramolecular potentials to heat conduction.     

Broadband dielectric spectroscopy of the inter- and intramolecular dynamics of a series of random polyester copolymers

Broadband dielectric spectroscopy (1–10⁶ Hz, 183–423 K) and differential scanning calorimetry are employed to analyze the inter- and intramolecular dynamics of a series of random copolymers based on poly(ethylene terephthalate) and poly(1,4-cyclohexylene dimethylene terephthalate). In addition to an interfacial relaxation (α*-process), three dielectric relaxation processes are observed: The α-relaxation (“dynamic glass transition”) and two secondary relaxations (β- and β*-relaxations). The α-relaxation depends sensitively on the composition of the copolymer and shows a rapid slowing down with increasing content of cyclohexylene dimethylene (CHDM) linkages. Besides the β-relaxation, attributed to local motion of the ester group, an additional process (β*-relaxation) is observed on introducing the CHDM linkages. Increasing the content of the latter reduces the strength of the β-relaxation strongly and increases its activation energy by more than 30%. This proves that owing to interactions between the cylohexylene rings and the ester group the β-relaxation no longer has local character only. Received: 28 September 2000 Accepted: 29 January 2001     

Quantum-Chemical and semiclassical calculations of intermolecular interactions of phospholipids

By use of empirical 0–1–6–12 atom–atom potential functions and the PCILOCC method intra- and intermolecular interactions of glycero–phosphoryl–ethanolamine model head groups in a planar layer crystal were calculated. Starting from investigations of the two-dimensional energy-contour diagrams the minima of energy as a function of all head group torsion angles were calculated using a gradient procedure. Within an interval of 15 kcal/mol above the energy of the global minimum we obtained about 30 local minima. These results demonstrate a high flexibility of the investigated phosphorylethanolamine head group in agreement with experiment. The ethanolamine moiety exists in enantiomeric conformations. With the torsion angles of the 0–1–6–12 energy minimization procedure PCILOCC calculations were carried out. These calculations yield the x-ray conformation as the most stable one (unit-cell stabilization energy = ?36.3 kcal/mol). The PCILOCC as well as the potential function calculations show that the conformation of phospholipid head groups in layer crystals is determined by intramolecular as well as by intermolecular interactions with neighboring phospholipid molecules.     

Modeling the interplay of inter- and intramolecular hydrogen bonding in conformational polymorphs

The predicted stability differences of the conformational polymorphs of oxalyl dihydrazide and ortho-acetamidobenzamide are unrealistically large when the modeling of intermolecular energies is solely based on the isolated-molecule charge density, neglecting charge density polarization. Ab initio calculated crystal electron densities showed qualitative differences depending on the spatial arrangement of molecules in the lattice with the greatest variations observed for polymorphs that differ in the extent of inter- and intramolecular hydrogen bonding. We show that accounting for induction dramatically alters the calculated stability order of the polymorphs and reduces their predicted stability differences to be in better agreement with experiment. Given the challenges in modeling conformational polymorphs with marked differences in hydrogen bonding geometries, we performed an extensive periodic density functional study with a range of exchange-correlation functionals using both atomic and plane wave basis sets. Although such electronic structure methods model the electrostatic and polarization contributions well, the underestimation of dispersion interactions by current exchange-correlation functionals limits their applicability. The use of an empirical dispersion-corrected density functional method consistently reduces the structural deviations between the experimental and energy minimized crystal structures and achieves plausible stability differences. Thus, we have established which types of models may give worthwhile relative energies for crystal structures and other condensed phases of flexible molecules with intra- and intermolecular hydrogen bonding capabilities, advancing the possibility of simulation studies on polymorphic pharmaceuticals.     

Macrocyclization of alpha-(alkynyloxy)silyl-alpha-diazoacetates by inter-/intramolecular

Thermally induced intra-/intermolecular [3 + 2] cycloaddition reaction sequences of alpha-(alkynyloxy)silyl-alpha-diazoacetates 1 lead to [3.3](1,4)pyrazolophanes (2)2 and higher cyclooligomers thereof [(2)n, n > 2]. In most cases, the cyclodimer was isolated by crystallization, while a complete separation of the mixture of the higher cyclooligomers was not possible. Solid state structures of cyclodimers (2b)2 and (2c)2, cyclotrimer (2b)3, and cyclotetramer (2e)4 were determined by X-ray diffraction analysis. Field-desorption mass spectra were used to characterize the cyclooligomer mixtures. The relative amounts of the cyclooligomers depend on the substitution pattern of the diazo compound. The cyclooligomerization reactions reported herein demonstrate, for the first time, the involvement of diazo functions in macrocyclization reactions via 1,3-dipolar cycloaddition.     

Pd-catalyzed inter- and intramolecular carbene transfer from group 6 metal-carbene complexes.

The use of group 6 metal-carbene complexes in inter- and intramolecular carbene transfer reactions has been studied. Thus, pentacarbonyl[(aryl)(methoxy)carbene]chromium(0) and tungsten complexes, 10, efficiently dimerize at room temperature in the presence of diverse Pd(0) and Pd(II)/Et(3)N catalysts. The effect of additives (PPh(3), AsPh(3), or SbPh(3)) on the nature and the isomeric ratio of the reaction products is negligible. The nature of the reaction products is more catalyst-dependent for metal carbenes 12 bearing alkyl groups attached to the carbene carbon. In these cases, either carbene ligand dimerization or beta-hydrogen elimination reactions are observed, depending on the catalyst. The carbene ligand dimerization reaction can be used to prepare conjugated polyenes, including those having metal moieties at both ends of the polyene system, as well as enediyne derivatives. The intramolecular carbene ligand dimerization of chromium bis-carbene complexes 28 and 30 allows the preparation of mono- and bicyclic derivatives, with ring sizes from six to nine members. For bis-carbene derivatives the beta-hydrogen elimination reaction is inhibited, provided that both metal centers are tethered by an o-xylylene group. Other alkyl complexes 32 form new mononuclear carbene complexes 37 or decompose to complex reaction mixtures. The results obtained in these reactions may be explained by transmetalation from Cr(0) to Pd(0) and the intermediacy of Pd-carbene complexes. Aminocarbene-chromium(0) complexes 15, need harsher reaction conditions to transfer the carbene ligand, and this transfer occurs only in the presence of deactivated olefins. The corresponding insertion/hydrolysis products 48 resulted in these cases. A catalytic cycle involving transmetalation from a chromacyclobutane to a palladacyclobutane is proposed to explain these results.