Donor and acceptor properties of the chromium tricarbonyl substituent in benzylic and homobenzylic anions, cations, and radicals

Both benzylic cations and anions are strongly stabilized by chromium tricarbonyl complexation, while benzylic radicals are largely unaffected. Density functional theory calculations were performed on primary, secondary, and tertiary benzylic species to explore the effect of substitution on the stabilizing ability of the chromium tricarbonyl moiety. Complexed 1-indanyl species were also examined to elucidate the effect of conformational restraint. It was found that the strong stabilization of benzylic anions and the slight destabilization of benzylic radicals by chromium tricarbonyl are insensitive to skeletal changes. Chromium-complexed benzylic cations, however, are highly sensitive to changes in the organic framework, with increased substitution or constriction of conformational mobility eroding the effect of the metal. 2-Indanyl species were also examined to study the effect of the chromium tricarbonyl fragment on homobenzylic species. It was found that the metal fragment stabilizes distant anions by field and inductive effects and cations by a direct interaction of the metal with the cationic carbon. Homobenzylic radicals, however, do not interact with the chromium tricarbonyl moiety and suffer a slight inductive destabilization.     

Effects of conformational flexibility of alkyl chains of cations on diffusion of ions in ionic liquids

Molecular dynamics simulations of ionic liquids [1-alkyl-3-methylimidazolium (alkyl = ethyl, butyl and hexyl), N-butylpyridinium, N-butyl-N,N,N-trimethylammonium and N-butyl-N-methylpyrrolidinium cations combined with the (CF(3)SO(2))(2)N(-) (TFSA) anion] show that the conformational flexibility of the alkyl chains in the cations is one of the important factors determining the diffusion of ions. Artificial constraint imposed on the internal rotation of alkyl chains significantly decreases the self-diffusion coefficients of cations and anions. The internal rotation of the C-N bond connecting the alkyl chain and the aromatic ring has large effects on the diffusion of ions in imidazolium and pyridinium based ionic liquids. The calculated self-diffusion coefficients of cations and anions decrease 20-40% by imposing the torsional constraint of the C-N bond. On the other hand the torsional constraint of the C-N bond does not largely change the diffusion of ions in the quaternary alkyl ammonium based ionic liquids. The conformational flexibility of the terminal C-C-C-C bond of the alkyl chains has large effects on the diffusion of ions in the quaternary alkyl ammonium based ionic liquids. The influence of the electrostatic interactions and the high density of ionic liquids on the diffusion of ions were studied. The electrostatic interactions have the paramount importance on the slow diffusion of ions in ionic liquids, while the high density of ionic liquids is also responsible for the slow diffusion. The electrostatic interactions and the high density of ionic liquids enhance the effects of the torsional constraint on the diffusion of ions, which suggests that the charge-ordering structure and small free volume originated in the strong electrostatic interactions are the causes of the significant effects of the conformational flexibility on the diffusion of ions in ionic liquids.     

The conformational stability of tactic poly(2-hydroxyethyl methacrylate) in aqueous salt solutions

The conformational stability of tactic poly(2-hydroxyethyl methacrylate) (PHEMA) in aqueous salt solutions was investigated by measurements of swelling, surface-free energy, and differential scanning calorimetry, as this polymer in water is sensitive in various electrolytes. In the case of inorganic salts, the major role for the salt effect is played by the anions, and the exposure of hydrophobic components at the PHEMA surface can be correlated with the increase of the degree of swelling. The influence of cations is considerably weaker. In the case of organic salts, tetraalkylammonium halides cause the chain extension more effectively with the increase of alkyl chain length in the cations. This result indicates that the breakdown of the hydrophobic parts in PHEMA provides an important clue on conformational stability. The amount of water molecules bound with the hydrophilic sites of tactic-PHEMA mainly depends on the chain extension and the hydration of cations. Since the sites in tactic-PHEMA influenced by the cation and the anion are different, their effects cause the conformational transition at a specific range of salt concentration. © 1993 John Wiley & Sons, Inc.     

Protein-cation interactions: structural and thermodynamic aspects

Cations are specifically recognized by numerous proteins. Cations may play a structural role, as cofactors stabilizing their binding partners, or a functional role, as cofactors activating their binding partners or being themselves involved in enzymatic reactions. Despite their small size, their charge density and their specific interaction with highly charged residues allow them to induce significant conformational changes on their binding proteins. The protein conformational change induced by cation binding may be as large as to account for the complete folding of a protein (as evidenced in Hepatitis C NS3 protease, or human rhinovirus 2A protease), and they may also trigger oligomerization (as in calcium-binding protein 1). Especially intriguing is the ability of cation-binding proteins of discriminating between very similar cations. In particular, calcium and magnesium are recognized by proteins with markedly different binding affinities and cause significantly different conformational changes and stabilization effects in the binding proteins (as in the fifth ligand binding repeat of the LDL receptor binding domain, calcium-binding protein 1, or parvalbumin). This article summarizes recent findings on the structural and energetic impact of cation binding to different proteins. A general framework can be envisaged in which cations can be considered as a special type of allosteric effectors able to modulate the functional properties of proteins, in particular the ability to interact with biological targets, by altering their conformational equilibrium.     

Polyfuryl(Aryl)alkanes and their derivatives. 6. Stereochemistry of intramolecular rotations about the C-C+ bonds in aryl(Alkyl)difurylcarbonium ions

It was demonstrated by dynamic ¹H NMR spectroscopy that for difurylmethyl and gem-difurylethyl cations conformational changes are realized through rotation of one of the furan rings, whereas in the case of aryldifurylmethyl cations conformational transformations take place as the simultaneous rotation of two aromatic rings; the correlated rotation of the two furan rings proceeds with smaller energy expenditures.For Communication 5 see [1].Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 4, pp. 450–455, April, 1993.     

Molekulare konformationen und hyperkonjugation: SiC und GeC hyperkonjugation und die konformation von β-silyl- und β-germyläthyl kation und anion

The conformational consequences of hyperconjugation in β-silyl- and β-germylethyl cations and anions have been investigated using an extended CNDO/2 approach. It is shown that the recently published conformational rules for β-substituted cations and anions fail in the cases considered here. The reason for their failure has been detected.     

Interaction of divalent metal cations and nucleotides: A computational study

In this study, the anionic phosphate group of nucleotides was found to be the best site to bind the divalent metal cations Be²⁺, Mg²⁺, Zn²⁺, Cd²⁺, Hg²⁺ and Pb²⁺ to form the most stable complexes. Molecular orbital calculations at the semiempirical level were performed on nucleotidemetal cation complexes to report energies of complexation reactions, geometrical parameters of complexes and charge distributions on the complexes. In the discussion, complexational preferences of divalent metal cations, the charge transfer involved in the binding of the metal cations to the phosphate anion of the nucleotides and their conformational effects are included.     

How Cations Change Peptide Structure

Specific interactions between cations and proteins have a strong impact on peptide and protein structure. Herein, we shed light on the nature of the underlying interactions, especially regarding effects on the polyamide backbone structure. This was done by comparing the conformational ensembles of model peptides in isolation and in the presence of either Li⁺ or Na⁺ by using state‐of‐the‐art density‐functional theory (including van der Waals effects) and gas‐phase infrared spectroscopy. These monovalent cations have a drastic effect on the local backbone conformation of turn‐forming peptides, by disruption of the hydrogen‐bonding networks, thus resulting in severe distortion of the backbone conformations. In fact, Li⁺ and Na⁺ can even have different conformational effects on the same peptide. We also assess the predictive power of current approximate density functionals for peptide–cation systems and compare to results with those of established protein force fields as well as high‐level quantum chemistry calculations (CCSD(T)).     

溶液pH和阳离子对端粒G-四链体DNA形成和结构的影响

采用电喷雾质谱和圆二色谱研究了溶液pH和阳离子对人类端粒G-四链体DNA的影响. ESI-MS和CD谱图表明, pH可以引起G-四链体DNA的构象转变和离解, 而K^＋, NH₄^＋,阳离子对G-四链体DNA的形成有着重要的促进作用.     

Photochemistry of Ethylbenzene Radical Cations in Low-Temperature Freonic Matrices

Two different conformers of ethylbenzene radical cations (or a mixture of both conformers) can be stabilized in various freonic matrices. The first conformer retains the geometry of the parent molecule, whereas the second one corresponds to minimum energy. It was shown that the photochemical reactions of the radical cations in various freons at 77 K were not accompanied by a change in their conformational state. The spectral characteristics of ethylbenzene radical cations and the quantum yields of photoinduced charge transfer reactions were determined. The reasons for stabilization of different conformers of the radical cations in different freonic matrices are discussed.     

Poly(thiophenes) derivatized with linear and macrocyclic polyethers: from cation detection to molecular actuation

The association of linear or macrocyclic polyethers with the electronic properties of the π-conjugated polythiophene backbone leads to functional conducting polymers that exhibit metal cation dependent electronic properties. Based on this concept, various classes of cation sensors have been proposed and investigated for almost two decades. The interactions of metal cations with linear or macrocyclic polyether functional groups lead to modifications of the electronic properties of the π-conjugated backbone through various mechanisms including direct electronic effects on a single conjugated chain, collective electrochemical processes, or conformational changes. Conjugated polymers and oligomers representative of these various processes are discussed with an emphasis on recent examples of derivatized conjugated systems in which the interactions between metal cations and polyether groups serve as driving force to create molecular motion in conjugated systems.     

FT-ICRMS distinguishes the mechanism of the charge state reduction for multiply charged protein cations admixed with redox reagents in ESI

Recently, we reported on a phenomenon in which multiply charged protein cations produced by electrospray ionization could be reduced to lower and narrower charge state distributions when admixed with reducing reagents 1,4-benzoquinone or quinhydrone. Circular dichroism spectra of the proteins indicated that secondary and tertiary structural changes upon addition of these reducing reagents were negligible, thus eliminating conformational effects as playing a role in the charge reduction mechanism. Furthermore, the extent of charge state reduction did not correspond with gas-phase basicities of the redox reagents, suggesting that solution-phase, and not gas-phase, behavior dominates the observed charge state reduction. The relatively low resolution of the triple quadrupole employed did not make it possible to distinguish isotopic distributions of the multiply charged cations in order to determine whether the observed phenomenon was the result of proton-transfer reactions between the multiply charged cations and the reducing reagent or because of electron transfer from the reducing reagent to the protein cations. Here, high-resolution ESI-Fourier transform ion cyclotron resonance mass spectrometry of several peptide amides in the presence of a redox reagent show isotopic distributions that are consistent only with the proton-transfer mechanism.     

13C n.m.r. of organosulphur compounds: II—13C chemical shifts and conformational analysis of methyl substituted thiacyclohexanes

¹³C n.m.r. spectra of methyl substituted thianes and thianium cations have been determined. The magnitude of the ¹³C substituent effects of an equatorial methyl group or of a gem-dimethyl grouping appear to depend in a systematic way on whether the carbon atom concerned is adjacent to, or removed from, the heteroatom. The shieldings are discussed in relation to the conformational properties of the thiane ring. Moreover, the average ¹³C substituent parameters obtained from conformationally biased systems are applied to potentially mobile systems to assess the position of the conformational equilibrium.     

Influence of metal cations on the intramolecular hydrogen-bonding network and pKa in phosphorylated compounds

The binding of the most common metal cations of cytoplasm (Li+, Na+, K+, Mg2+ and Ca2+) to a model molecule having an intramolecular hydrogen-bonding network, myo-inositol-2-monophosphate, was studied using first principles. A strong correlation between the conformation of metal inositol phosphate complexes with the type of metal cation, degree of deprotonation state, and the surrounding environment has been observed. On the basis of the hydrogen-bonding network analysis of the cation-phosphate complexes (Mn+-Ins(2)P1), the alkali cations show little effect on the conformational preference while the conformational preference for the binding of the alkaline earth cations is pH-dependent and solvent-dependent. For example, these calculations predict that Mg2+-Ins(2)P1(0) and Mg2+-Ins(2)P1(2-) favor the 1a/5e form while Mg2+-Ins(2)P1(1-) favors the 5a/1e conformation. The Ca2+-Ins(2)P1(2-) complex prefers the 1a/5e conformation in the gas phase and in a nonpolar protein environment, but inverts to the 5a/1e conformation upon entering the polar aqueous phase. The binding affinities of the cations and the pK(a) values for the cation-phosphate complexes are derived from thermodynamical analysis.     

Stereochemical memory versus Curtin-Hammett behavior in the rearrangement of 1,3-cyclopentanediyl radical cations derived from housanes through structural effects on conformational control

The electron-transfer-catalyzed rearrangement of the housanes 1 affords regioselectively the two cyclopentenes 2 and 3 by 1,2-migration of a group at the methano bridge. Appropriate ring annelation in the intermediary cyclopentane-1,3-diyl radical cation 1(*+) changes the stereochemical course of the rearrangement from complete stereoselectivity (stereochemical memory) for the structurally simple housane 1b to partial loss of stereoselectivity through competing conformational interconversion for the tricyclic housane 1c. Additional cyclohexane annelation, as in the tetracyclic housane 1a, results in complete loss of stereocontrol through Curtin-Hammett behavior, as substantiated by the viscosity dependence on the product ratio of the rearrangement. Whereas in the radical cations 1b(*+) and 1c(*+) the 1,2-shifts (k(2) and k(3)) are faster than the conformational anti <==> syn change (k(1), k(-1)), the reverse applies for the radical cation 1a(*+). Such structural manipulation of conformational effects in radical cation rearrangements has hitherto not been documented.     

Interaction study of a lysozyme‐binding aptamer with mono‐ and divalent cations by ACE

Binding between an aptamer and its target is highly dependent on the conformation of the aptamer molecule, this latter seeming to be affected by a variety of cations. As only a few studies have reported on the interactions of monovalent or divalent cations with aptamers, we describe herein the use of ACE in its mobility shift format for investigating interactions between various monovalent (Na⁺, K⁺, Cs⁺) or divalent (Mg²⁺, Ca²⁺, Ba²⁺) cations and a 30‐mer lysozyme‐binding aptamer. This study was performed in BGEs of different natures (phosphate and MOPS buffers) and ionic strengths. First, the effective charges of the aptamer in 30 mM ionic strength phosphate and MOPS (pH 7.0) were estimated to be 7.4 and 3.6, respectively. Then, corrections for ionic strength and counterion condensation effects were performed for all studies. The effective mobility shift was attributed not only to these effects, but also to a possible interaction with the buffer components (binary or ternary complexes) as well as possible conformational changes of the aptamer. Finally, apparent binding constants were calculated for divalent cations with mathematical linearization methods, and the influence of the nature of the BGE was evidenced.     

Investigation of guanosine-quartet assemblies by vibrational and electronic circular dichroism spectroscopy, a novel approach for studying supramolecular entities

The self-assembly of guanosine-5'-hydrazide G-1 in D(2)O, in the presence and absence of sodium cations, has been investigated by chiroptical techniques: electronic (ECD) and the newly introduced vibrational (VCD) circular dichroism spectroscopy. Using a combination of ECD and VCD with other methods such as IR, electron microscopy, and electrospray ionization mass spectrometry (ESI-MS) it was found that G-1 produces long-range chiral aggregates consisting of G-quartets, (G-1)(4), subsequently stacked into columns, [(G-1)(4)](n), induced by binding of metal cations between the (G-1)(4) species. This process, accompanied by gelation of the sample, is highly efficient in the presence of an excess of sodium cations, leading to aggregates with strong quartet-quartet interaction. Thermally induced conformational changes and conformational stability of guanosine-5'-hydrazide assemblies were studied by chiroptical techniques and the melting temperature of the hydrogels formed was obtained. The temperature-dependent experiments indicate that the long-range supramolecular aggregates are dissociated by increasing temperature into less ordered species, monomers, or other intermediates in equilibrium, as indicated by MS experiments.     

Conformational templation in a singly bridged calix[7]arene derivative induced by alkali metal cations

The first examples of alkali metal cation conformational templation of a calix[7]arene derivative were found in the alkali salts of 1,4-calix[7]crown-4, which were obtained by its treatment with the corresponding alkali metal carbonates. Competitive experiments showed that potassium and rubidium cations give the most effective templation, with a slight preference for the former. Experimental results and Monte Carlo conformational searches indicated that the cation interacts with all O-atoms including those of the crown-4 bridge.     

A tale of two ions: the conformational landscapes of bis(trifluoromethanesulfonyl)amide and N,N-dialkylpyrrolidinium

The conformational landscapes of two commonly used ionic liquid ions, the anion bis(trifluoromethanesulfonyl)amide (Ntf2) and the cations N-propyl- and N-butyl-N-methylpyrrolidinium, were investigated using data obtained from Raman spectroscopy, molecular dynamics, and ab initio techniques. In the case of Ntf2, the plotting of three-dimensional potential energy surfaces (PES) and the corresponding molecular dynamics (MD) simulations confirmed the existence of two stable isomers (each existing as a pair of enantiomers) and evidenced the nature of the anion as a flexible, albeit hindered, molecule capable of interconversion between conformers in the liquid state, a result confirmed by the Raman data. In the case of the N,N-dialkylpyrrolidinium cations, the PES show a much more limited conformational behavior of the pyrrolidinium ring (pseudorotation). Nevertheless, such pseudorotation produces two stable isomers with the propyl and butyl side chains in completely different positions (axial-envelope and equatorial-envelope conformations). This result was also confirmed by Raman spectra analyses and MD simulations in the liquid phase. The implications of the conformational behavior of the two types of ions are discussed in terms of the solvation properties of the corresponding ionic liquids.     

The Effect of Phenyl Substitutions on Microstructures and Dynamics of Tetraalkylphosphonium Bis(trifluoro- methylsulfonyl)imide Ionic Liquids

Extensive atomistic simulations demonstrated that a gradual substitution of hexyl chains with phenyl groups in tetraalkylphosphonium cations results in remarkable changes in hydrogen bonding interactions, liquid structures and scattering structural functions, and rotational dynamics of hexyl chains and phenyl groups in tetraalkylphosphonium bis(trifluoromethylsulfonyl)imide ionic liquids. Hydrogen donor sites in hexyl chains present competitive characteristics with those in phenyl groups in coordinating anions, as well as their continuous and intermittent hydrogen bonding dynamics. Cation-cation and anion-anion spatial correlations show concomitant shift to short distances with decreased peak intensities with variations of cation structures, whereas cation-anion correlations have a distinct shift to large radial distances due to decreased associations of anions with neighboring cations. These microstructural changes are qualitatively manifested in shifts of prominent peaks for prevalent charge alternations and adjacency correlations between ion species in scattering structural functions. Meanwhile, rotational dynamics of hexyl chains speed up, which, in turn, slow down rotations of phenyl groups, whereas anions exhibit imperceptible changes in their rotational dynamics. These computational results are intrinsically correlated with conformational flexibilities, molecular sizes, and steric hindrance effects of phenyl groups in comparison with hexyl chains, and constrained distributions of anions around cations in heterogeneous ionic environments.