Azolium-linked cyclophanes: a comprehensive examination of conformations by 1H NMR spectroscopy and structural studies

The synthesis and characterization of a series of azolium-linked cyclophanes are reported. The cyclophanes consist of two azolium groups (17 examples) or three imidazolium groups (1 example) linked to two benzenoid units (benzene, naphthalene, p-xylene, mesitylene, 1,2,3,4- and 1,2,4,5-tetramethylbenzene, 2,6-pyridine, and p-tert-butylphenol) via methylene groups. Cyclophanes containing ortho-, meta-, and para-substitution patterns in the benzenoid units were examined. The conformations of the cyclophanes were examined in solution by variable-temperature NMR studies and in the solid state by crystallographic studies. The p-cyclophanes and mesitylene-based m- and o/m-cyclophanes are rigid on the NMR time scale, as indicated by sharp (1)H NMR spectra at all accessible temperatures. The non-mesitylene-based m-cyclophanes and the o-cyclophanes are fluxional on the NMR time scale at high temperatures, but in most cases, specific conformations can be "frozen out" at low temperatures. Many structures deduced from solution studies were consistent with those in the solid state.     

The effects of denaturants on protein conformation and behavior at air/solution interface

In this study, we discuss the interfacial behavior of five proteins with different conformational character, and each is investigated in native and denatured states. The protein molecules are layered and spread onto the air/solution interfaces to form protein monolayer. The surface pressure-time (Pi(t)) and surface pressure-area per molecule (Pi-A) isotherms were measured by using the Langmuir-Blodgett (LB) balance consisted of a Nima trough system. The differences between monolayered protein's behaviors at air/solution interface indicate that denaturants, such as urea, guanidinium chloride and dithiothreitol, have different effects on conformational changes of proteins. Additionally, the interfacial behavior of the proteins in our study provides a fundamental profile about the protein structural stability and implies industrial applications in protein refolding process.     

Anion mediated,tunable isoguanosine self-assemblies: decoding the conformation influence and solvent effects

Systematic investigations were performed with various substituted groups at C8 purine and ribose. A series of isoG analogs, C8-phenyl substituted isoG were synthesized and applied for Cs⁺ coordination. The structural proximity between purine and ribose limited pentaplex formation for C8-phenyl substituted isoG derivatives. Based on this observation, deoxy isoG derivative with modification on ribose (tert-butyldimethylsilyl ether) was applied to assemble with the Cs⁺ cation. Critical solvent (CDCl₃ and CD₃CN) and anion (BPh₄⁻, BARF⁻, and PF₆⁻) effects were revealed, leading to the controllable formation of various stable isoG pentaplexes, including singly charged decamer, doubly charged decamer, and 15-mer, etc. Finally, the X-ray crystal structure of [isoG₂₀Cs₃]³⁺(BARF⁻)₃ was successfully obtained, which is the first example of multiple-layer deoxy isoG binding with the Cs⁺ cation, providing solid evidence of this new isoG ionophore beyond two-layer sandwich self-assembly.

The first example of multiple-layer deoxy isoG self-assembly was characterized by X-ray crystal structure. Critical solvent and anion effects were revealed, leading to the controllable formation of various stable isoG assemblies.     

Effect of a solvent on the solution behavior of Teflon-42 and the structure of related films

The viscosity characteristics of dilute and concentrated solutions of Teflon-42 in acetone, DMF, DMAA, N-methylpyrrolidone, and trimethyl phosphate have been studied. Films based on Teflon-42 prepared by precipitation from concentrated aqueous solutions are investigated by IR spectroscopy and X-ray analysis. The analysis of intrinsic viscosity and viscosity of concentrated solutions shows that, with respect to Teflon-42, solvent quality changes in the following order: acetone > DMF > DMAA > trimethyl phosphate ≥ N-methylpyrrolidone. Films prepared from polymer solutions in various solvents are characterized by a highly crystalline structure (the degree of crystallinity is ～70%) that involves three polymorphic modifications.     

Influence of solvent structure on the conformation of the native DNA molecule

The investigation of the factors determining the formation and stability of the higher biopolymers structures is one of the most important trends of the development of molecular biophysics. A feature common to most macromolecular systems under physiological conditions is that they function in an aqueous environment. Thus, it is natural to assume that the peculiarities of biological macromolecules structures and their functional activity as well are closely related to the specific properties of such a unique solvent as water. The investigations of the conformational changes of biopolymer, induced by dehydration of the macromolecule, give information about the nature of the forces stabilizing its structure. The dehydration of the macromolecule in solution can be attained by addition of a nonaqueous cosolvent. Generally low-molecular-weight aliphatic alcohols, amides, and amines are used as a nonaqueous component. At present a vast number of experimental and theoretical data concerning the properties of water and aqueous systems are available. The specificity of water as a solvent arises primarily from the spatial hydrogen-bonded structure. The addition of a nonaqueous component exerts changes in this structure, which evolve to the singularities of the physical characteristics of water-nonelectrolyte mixtures. It is generally assumed that nonelectrolytes may be divided, according to their effect on the spatial water structure, largely into two basic classes: (1) the structure makers, i.e., the compounds of aliphatic alcohols type; (2) the structure breakers, i.e., the compounds of urea type. The agents belonging to the first class show a stabilizing effect in the range of low nonelectrolyte content. At a certain critical concentration, C_crit, characteristic of each substance, the nonaqueous solute molecules leave the cavities of the spatial water structure which leads to a disruption of the latter. The agents belonging to the second class exert a structure-breaking effect even in the range of extremely low concentrations, which arises from their high competitive ability for hydrogen bonding.     

Tryptophan-derived peptides. 1: Crystal structure and solution conformation of Boc-Gly-Trp-Ala-OtBu

The solid-state structure of Boc-Gly-Trp-Ala-OBu^t was determined by single-crystal X-ray diffraction analysis. The tripeptide gave crystals belonging to the orthorhombic systemP2₁2₁2₁ and at 122.0(5) K:a=11.0663(12),b=14.107(2),c=17.275(2) Å,V=2697.0(5) ųZ=4,R(F)=0.0259, andR _w(F)=0.0695. The peptide adopts a type-I-turn in the solid state with a single, rather weak, intramolecular hydrogen bond between the Boc-CO and Ala-NH groups (NO 3.082(1) Å, <NHO 167(1)°). The conformation of the Boc-Gly-Trp-Ala-OBu^t peptide has also been studied by¹H NMR spectroscopy. The solvent and temperature dependencies of NH chemical shifts suggests that this hydrogen bond is broken and that all amide protons are solvent exposed in CDCl₃ and (CD₃)₂SO.     

Conformations and solution structure of polyelectrolytes in poor solvent

Using extensive Molecular Dynamics (MD) simulations we study the behavior of polyelectrolytes in poor solvents, where we take explicitely care of the counterions. The resulting pearl-necklace structures are subject to strong conformational fluctuations, only leading to small signatures in the form factor, which is a severe obstacle for experimental observations. In addition we study how the necklace collapses as a function of Bjerrum length. At last we demonstrate that the position of the first peak in the inter-chain structure factor varies with the monomer density close to for all densities. This is in strong contrast to polyelectrolyte solutions in good solvent.     

Solid state structure and solution conformation of a macrobicyclic cyclophane

X-ray crystallographic structure determination of the macrobicyclic cyclophane L¹ reveals a compact structure involving close edge-to-face approach of aromatic rings; ¹H nmr shows that this is also the solution conformation.     

Polyelectrolyte behavior and conformation of poly-L-methionine S-methylsulfonium salts in aqueous solution

The influence of the species of counterion on the polyelectrolyte behavior and the conformation of poly-L -methionine S-methylsulfonium salts in aqueous solution was studied by viscometric, electrochemical, and optical measurements. The degree of binding of small counterions to charged polyions increases in the sequence: chloride ? bromide < iodide < thiocyanate. The conformations of chloride and bromide salts are independent of polymer concentration. On the contrary, iodide and thiocyanate salts indicate a conformational transition, probably from a random-coil conformation to an intermolecularly stabilized β-form, with the increase of polymer concentration. The results suggest the existence of a strong specific interaction between counterion and macroion in iodide and thiocyanate salt solutions at high polymer concentration.     

The effects of solution structure on the surface conformation and orientation of a cysteine-terminated antimicrobial peptide cecropin P1

The surface structure of an antimicrobial peptide, cecropin P1, immobilized to a gold surface via a terminal cysteine residue was investigated. Using reflection-absorption infrared spectroscopy, surface plasmon resonance, and X-ray photoelectron spectroscopy, the effects of pH, solution conformation, and concentration on the immobilized peptide conformation, average orientation, and surface density were determined. Under all conditions investigated, the immobilized peptides were α-helical in a predominately flat, random orientation. The addition of the reducing agent Tris(2-carboxyethyl) phosphine hydrochloride to the buffer resulted in a twofold increase in immobilized peptide surface density.     

p-Benzoquinone in aqueous solution: Stark shifts in spectra, asymmetry in solvent structure

Results from a simulation of p-benzoquinone (PBQ) in water is presented. An explicit solvent representation is used together with a multiconfigurational ab initio quantum chemical method. The electronic n --> pi* transitions are studied in aqueous solution and the two such transitions are both blue-shifted but to different degree. Both non-equilibrium and many-body effects are found to have decisive influence on the solvation: despite stronger hydrogen bonding between solute and solvent in an excited state than in the ground state, there is a blue-shift, and the solvent structure around the non-polar PBQ is asymmetric, which is argued to come from special many-body effects. The unusual result of strengthened hydrogen bonds in the excited state that follows from an excitation of a non-bonding electron on a proton acceptor, is explained by the near-linear Stark shift that is present in the transition.     

A comprehensive study of self-assembled monolayers of anthracenethiol on gold: solvent effects, structure, and stability

The formation and molecular structure of self-assembled monolayers (SAMs) of anthracene-2-thiol (AnT) on Au(111) have been characterized by reflection adsorption infrared spectroscopy, thermal desorption spectroscopy, X-ray photoelectron spectroscopy, near-edge X-ray absorption spectroscopy, scanning tunneling microscopy, and low energy electron diffraction. It is demonstrated that highly ordered monolayer films are formed upon immersion, but their quality depends critically on the choice of solvents and rinsing conditions. The saturated monolayer is characterized by a closed packed arrangement of upright standing molecules forming a (2 x 4)rect unit cell. At about 450 K a partial desorption takes place and the remaining molecules form a dilute (4 x 2)-phase with an almost planar adsorption geometry, while further heating above 520 K causes a thermally induced fragmentation. According to their different densities both phases reveal very diverse chemical reactivities. Whereas the saturated monolayer is stable and inert under ambient conditions, the dilute phase does not warrant any protection of the sulfur headgroups which oxidize rapidly in air.     

Imidazolium ion-terminated self-assembled monolayers on Au: effects of counteranions on surface wettability

Self-assembled monolayers presenting imidazolium ions at the tail ends (SAMIMs) having different counteranions have been prepared on Au, and the measurement of water contact angles of the surfaces proved to be an extremely valuable simple technique for quantifying the effects of counteranions on hydrophilicity and hydrophobicity of SAMIMs, which will be extrapolated to the water miscibility of the related ionic liquids.     

Counterion and solvent effects on the dilute solution viscosity of polystyrene ionomers

We present an analysis of data on the intrinsic viscosity [η] of sulfo-polystyrene ionomers in several solvents for a variety of sulfonation levels and counterions. For solvents of low dielectric constant, 2 < ε < 18, [η] decreases from the base polymer value [η]₀ with increasing substitution level. This behavior was attributed to intramolecular association of ionic dipoles. The ratio [η]/[η]₀ was found to depend on a single reduced variable α_Aα_Sx, where x is the fractional substitution, α_A depends only on the counterion, and α_S ∝ ε^?1 depends only on the solvent. For solvents of high dielectric constant, 36 < ε < 47, [η] increases approximately as x³, and counterion effects are small. This behavior was attributed to ionic dissociation, giving rise to a polyelectrolyte effect. Implications of the low ε results are discussed in relation to association-induced gelation behavior and possible generalizations of the reduced variables approach.     

DFT,solution, and crystal conformation of eremophilanolides

The minimum energy conformation of five eremophilanolides (1–5) from the tubercles of Psacalium paucicapitatum was calculated using density functional theory (DFT) at the B3LYP/6-31G¹ level. Comparison of the experimental ¹H–¹H coupling constant values of 1–5 with those generated employing a generalized Karplus-type relationship using dihedral angles extracted from the DFT calculation and from the crystal structures for 1 and 3–5 shows good agreement. The A ring of 1–5 adopts an almost perfect chair conformation with the Me-14 group in an axial position and the Me-15 in an equatorial position.     

Polyphosphate ions encapsulated in oxothiomolybdate rings: synthesis, structure, and behavior in solution

Cyclic oxothiomolybdates containing polyphosphate ions were prepared by simple reactions in aqueous medium of the corresponding polyphosphate ions and the cyclic precursor K(2)I(2)Mo(10)S(10)O(10)(OH)(10)(OH(2))(5).15H(2)O. K(5)[Cl(P(2)O(7)]Mo(12)S(12)O(12)(OH)(12)(H(2)O)(4)].22H(2)O (1) was isolated from concentrated chloride solution (2.5 mol.L(-1)). 1 reveals a remarkable complex containing two different substrates encapsulated in a dodecanuclear ring, a H-bonded Cl(-) ion, and a covalently bonded [P(2)O(7)] group. The chloride ion in 1 can be selectively removed for a monohydrogenophosphate group yielding K(6)[(HPO(4))(P(2)O(7))Mo(12)S(12)O(12)(OH)(12)(H(2)O)(2)].19H(2)O (2), a mixed species containing a [P(2)O(7)] and a [HPO(4)] group. The substitution is accompanied by a significant change of the ring, which adopts a "pear-shape" conformation. In the presence of triphosphate ion, the "heart-shaped" decanuclear ring Rb(3)[(H(2)P(3)O(10))Mo(10)S(10)O(10)(OH)(10)].17.5H(2)O (3) is formed containing a linear [P(3)O(10)] group intimately embedded in the inorganic cyclic host. The three compounds were structurally characterized by single-crystal X-ray diffraction. The behaviors of 1, 2, and 3 in solution were studied by (31)P NMR. Variable temperature experiments, supported by a two-dimensional COSY (31)P experiment, revealed that the supramolecular interaction existing between the chloride ion and the ring in solid 1 is maintained in solution. Nevertheless, 1 remains labile, and successive equilibria were evidenced and interpreted as an ion-pair association involving a halide ion (Cl, Br, or I), responsible for the conformational change of the [P(2)O(7)] group within the cavity. The influence of the nature of the halide guest (Cl(-), Br(-), and I(-)) on the successive equilibria was studied, and the thermodynamic constant related to the postulated equilibrium was determined. The stability of the supramolecular association decreases in the order Cl > Br > I. In solution, a phosphate exchange is observed for 2 while for 3 the absence of temperature dependence of the (31)P NMR spectrum confirms the conformation of the host-guest system is blocked. Elemental analysis and infrared characterizations are also supplied.     

Synthesis,structure, and dynamic behavior in solution of arylamino-1,3,5-triazines

Ten unsymmetrically substituted arylamino-1,3,5-triazines were synthesized and studied by dynamic NMR spectroscopy. The free energies of the hindered rotation ΔG^≠?are in 59–77 kJ mol^{? 1} range. Using difference-mode NOE NMR experiments, the structures of the major and minor rotation isomers were proved. The DFT B3LYP/6-31G* calculations were performed. The difference between the calculated rotation barriers and the experimental values obtained by line shape analysis is less than 7.6 kJ mol^?1. The height of the rotation barrier varies in a 18 kJ mol^?1 range depending on the substituents in the triazine ring.     

Molecular switch triggered by solvent polarity: synthesis,Acid-base behavior,alkali metal ion complexation,and crystal structure

The synthesis and characterization of the new tetraazamacrocycle L, bearing two 1,1'-bis(2-phenol) groups as side-arms, is reported. The basicity behavior and the binding properties of L toward alkali metal ions were determined by means of potentiometric measurements in ethanol/water 50:50 (v/v) solution (298.1+/-0.1 K, I=0.15 mol dm(-3)). The anionic H(-1)L(-) species can be obtained in strong alkaline solution, indicating that not all of the acidic protons of L can be removed under the experimental conditions used. This species behaves as a tetraprotic base (log K(1)=11.22, log K(2)=9.45, log K(3)=7.07, log K(4)=5.08), and binds alkali metal ions to form neutral [MH(-1)L] complexes with the following stability constants: log K(Li)=3.92, log K(Na)=3.54, log K(K)=3.29, log K(Cs)=3.53. The arrangement of the acidic protons in the H(-1)L(-) species depends on the polarity of the solvents used, and at least one proton switches from the amine moiety to the aromatic part upon decreasing the polarity of the solvent. In this way two different binding areas, modulated by the polarity of solvents, are possible in L. One area is preferred by alkali metal ions in polar solvents, the second one is preferred in solvents with low polarity. Thus, the metal ion can switch from one location to the other in the ligand, modulated by the polarity of the environment. A strong hydrogen-bonding network should preorganize the ligand for coordination, as confirmed by MD simulations. The crystal structure of the [Na(H(-1)L)].CH(3)CN complex (space group P2(1)/c, a=12.805(1), b=20.205(3), c=14.170(2) A, beta=100.77(1) degrees, V=3601.6(8) A(3), Z=4, R=0.0430, wR2=0.1181), obtained using CH(2)Cl(2)/CH(3)CN as mixed solvent, supports this last aspect and shows one of the proposed binding areas.     

Arylbiphenylene atropisomers: structure, conformation, stereodynamics, and absolute configuration

Anti and syn conformers, due to restricted sp(2)-sp(2) bond rotation, were detected in hindered 1,8-diarylbiphenylenes, the aryl moieties being phenyl groups bearing 0micron-alkyl substituents such as Me, Et, i-Pr, and t-Bu. By means of low-temperature NOE experiments, the corresponding structures were assigned and were found to be in agreement with the results of single-crystal X-ray diffraction. The interconversion barriers of these conformers were determined by line-shape simulation of the variable-temperature NMR spectra and the experimental values were reproduced satisfactorily by DFT calculations. In the case of the bulkiest aryl substituent investigated (i.e., 2-methylnaphthalene), the syn and anti atropisomers were stable enough as to be separated at ambient temperature. The two enantiomers (M,M and P,P) of the isomer anti were also isolated by enantioselective HPLC, and the theoretical interpretation of the corresponding CD spectrum allowed the absolute configuration to be assigned.