Induced-fit molecular recognition with water-soluble cavitands

Synthesis of novel water-soluble cavitands 1 and 2 and their complexes--the caviplexes--is described. The solubility in water derives from four primary ammonium groups on the lower rim and eight secondary amide groups on the upper rim. Cavitands 1 and 2 exist as D2d velcraplex dimers in aqueous solution but the addition of lipophilic guests 15-24 induces conformational changes to the vase-like structures. The internal cavity dimensions are 8 x 10 A, and the exchange rates of guests in the caviplexes are slow on the NMR time-scale (room temperature and 600 MHz). The direct observation of bound species and the stoichiometry of the complexes is reported. The association constants (Ka) between 0.4 x 10(-1) (-deltaG295= 0.7 kcalmol(-1)) and 1.4 x 10(2)M(-1) (-deltaG295=2.9 kcalmol(-1)) in D2O and 1.4 x 10(1)(-deltaG295= 1.7 kcalmol(-1)) and 2.8 x 10(4)M(-1)(-deltaG295=6.0 kcalmol(-1)) in [D4]methanol for aliphatic guests 16-24 were determined. Guest exchange rates of the new hosts 1 and 2 are considerably slower than rates observed for typical open-ended cavities in aqueous solution.     

Gamma-cyclodextrin forms a highly compressible complex with 1-adamantanecarboxylic acid

We report temperature-dependent ultrasonic velocimetric and densimetric data on changes in volume, expansibility, and adiabatic compressibility associated with the binding of 1-adamantanecarboxylic acid (AD) to gamma-cyclodextrin (gamma-CD). We compare these results with our previous data on the binding of AD to beta-cyclodextrin (beta-CD) [Taulier, N.; Chalikian, T.V.J. Phys. Chem. B 2006, 110, 12222-12224]. The comparison reveals that, in contrast to the tight AD-beta-CD complex with little void space left inside the cavity, AD forms a loose complex with gamma-CD with approximately 30 A3 of void space between the guest molecule and the inner walls of the cavity. The presence of the void renders the AD-gamma-CD complex highly compressible; the intrinsic coefficient of compressibility of the AD-gamma-CD complex is 37x10(-6) bar(-1) at 18 degrees C and decreases to 23x10(-6) bar(-1) at 55 degrees C. Such large compressibility is suggestive of only weak contacts between the interacting AD and gamma-CD atomic groups in the cavity. Our results are consistent with the notion that the AD-gamma-CD complex is predominantly stabilized by the hydrophobic effect with only modest contribution from intermolecular van der Waals interactions. This notion is in contrast to the AD-beta-CD complex which is stabilized by strong host-guest van der Waals interactions in addition to the hydrophobic effect.     

Internal energy distribution of peptides in electrospray ionization : ESI and collision-induced dissociation spectra calculation

The internal energy of ions and the timescale play fundamental roles in mass spectrometry. The main objective of this study is to estimate and compare the internal energy distributions of different ions (different nature, degree of freedom 'DOF' and fragmentations) produced in an electrospray source (ESI) of a triple-quadrupole instrument (Quattro I Micromass). These measurements were performed using both the Survival Yield method (as proposed by De Pauw) and the MassKinetics software (kinetic model introduced by Vékey). The internal energy calibration is the preliminary step for ESI and collision-induced dissociation (CID) spectra calculation. meta-Methyl-benzylpyridinium ion and four protonated peptides (YGGFL, LDIFSDF, LDIFSDFR and RLDIFSDF) were produced using an electrospray source. These ions were used as thermometer probe compounds. Cone voltages (V(c)) were linearly correlated with the mean internal energy values () carried by desolvated ions. These mean internal energy values seem to be slightly dependent on the size of the studied ion. ESI mass spectra and CID spectra were then simulated using the MassKinetics software to propose an empirical equation for the mean internal energy () versus cone voltage (V(c)) for different source temperatures (T): < E(int) > = [405 x 10(-6) - 480 x 10(-9) (DOF)] V(c)T + E(therm)(T). In this equation, the E(therm)(T) parameter is the mean internal energy due to the source temperature at 0 V(c).     

Measurements of the thickness compressibility of an n-octadecyltriethoxysilane monolayer self-assembled on mica

The surface forces apparatus technique and the Johnson-Kendall-Roberts theory were used to study the elastic properties of an n-octadecyltriethoxysilane self-assembled monolayer (OTE-SAM) on both untreated and plasma-treated mica. Our aim was to measure the thickness compressibilities of OTE monolayers on untreated and plasma-treated mica and to estimate their surface densities and phase-states from the film compressibility. The compressibility moduli of OTE are (0.96 +/- 0.02) x 10(8) N/m(2) on untreated mica and (1.24 +/- 0.06) x 10(8) N/m(2) on plasma-treated mica. This work suggests that the OTE phase-state is pseudocrystalline. In addition, the results from the compressibility measurements in water vapor suggest that the OTE-SAM on both untreated and plasma-treated mica is not homogeneous but rather contains both crystalline polymerized OTE domains and somewhat hydrophilic gaseous regions.     

Influence of the pressure on the properties of chromatographic columns. I. Measurement of the compressibility of methanol-water mixtures on a mesoporous silica adsorbent

The compressibilities of aqueous solutions of methanol or acetonitrile containing 0, 20, 40, 60, 80 and 100% (v/v) organic solvent were measured with a dynamic chromatographic method. The elution volumes of thiourea samples (2 microL) in these solutions were measured at different average column pressures, adjusted by placing suitable capillary restrictors on-line, after the detector. The reproducibility of the measurements was better than 0.2%. In the range of average pressures studied (10-350 bar), the maximum change in elution volume of thiourea is 1.3% (in pure water) and 4.0% (in pure methanol). This difference is due to the different compressibilities of these pure solvents. For mixtures, the plots of the elution volume of thiourea versus the pressure are convex downward, which is inconsistent with the opposite curvature predicted by the classical Tait model of liquid compressibility. This difference is explained by the variation of the amount of thiourea adsorbed with the pressure. The deconvolution of the two effects, adsorption of thiourea and solvent compressibility, allows a fair and consistent determination of the compressibilities of the methanol-water mixtures. A column packed with non-porous silica particles was also used to determine the compressibility of methanol-water and acetonitrile-water mixtures. A negative deviation by respect to ideal behavior was observed.     

Pressure and temperature dependence of hydrophobic hydration: volumetric, compressibility, and thermodynamic signatures

The combined effect of pressure and temperature on hydrophobic hydration of a nonpolar methanelike solute is investigated by extensive simulations in the TIP4P model of water. Using test-particle insertion techniques, free energies of hydration under a range of pressures from 1 to 3000 atm are computed at eight temperatures ranging from 278.15 to 368.15 K. Corresponding enthalpy, entropy, and heat capacity accompanying the hydration process are estimated from the temperature dependence of the free energies. Partial molar and excess volumes calculated using pressure derivatives of the simulated free energies are consistent with those determined by direct volume simulations; but direct volume determination offers more reliable estimates for compressibility. At 298.15 K, partial molar and excess isothermal compressibilities of methane are negative at 1 atm. Partial molar and excess adiabatic (isentropic) compressibilities are estimated to be also negative under the same conditions. But partial molar and excess isothermal compressibilities are positive at high pressures, with a crossover from negative to positive compressibility at approximately 100-1000 atm. This trend is consistent with experiments on aliphatic amino acids and pressure-unfolded states of proteins. For the range of pressures simulated, hydration heat capacity exhibits little pressure dependence, also in apparent agreement with experiment. When pressure is raised at constant room temperature, hydration free energy increases while its entropic component remains essentially constant. Thus, the increasing unfavorability of hydration under raised pressure is seen as largely an enthalpic effect. Ramifications of the findings of the authors for biopolymer conformational transitions are discussed.     

Hole burning spectroscopy of ribonuclease A

We present pressure tuning hole burning experiments with the enzyme ribonuclease A using the UV-absorbing amino acid tyrosine as a probe. We show that, at 2 K, the protein is intact, and that at least four different regions which we associate with different tyrosine sites can be distinguished through their specific response to pressure. For one site we could determine the compressibility to 0.15 GPa(-1). Upon denaturing the protein with guanidine hydrochloride, one of the tyrosine sites is preserved to a large extent. Reducing the sulfur bonds has a more drastic effect: the tyrosine sites lose most of their individual features and their compressibilities come close to that of tyrosine in solution.     

Polarographic analysis of the mixed-ligand system Cu(II)-glycine-glycinate

The polarographic method has been applied to the study of the mixed-ligand system Cu(II)-glycine-glycinate, in aqueous medium, at I = 1.0M (NaClO(4)) and 25 -/+ 0.1 degrees . The stabilization of the mixed complex [CuG(G(-))](+) has been made clear and its stability constant (beta(11) = 1 x 10(9)) has been determined. The stability constants of the complexes [CuG]I(2+) (beta(10) = 17), [CuG(2)](2+) (beta(20) = 230), [Cu(G(-))](+) (beta(01) = 2.1 x 10(8)) and [Cu(G(-))(2)] (beta(02) = 1.7 x 10(15)) have also been calculated.     

Evidence of PVT anomaly boundaries of water at high pressure from compression and NaCl.2H2O dehydration experiments

Isothermal compression experiments on water have been performed between 0 to 80 degrees C and up to 1.3 GPa pressure. The compressibilities derived from the water compression experiments reveal a nonsmooth PVT behavior forming two anomaly boundaries. These boundaries originate at the melting line of ice III at about 0.25 GPa/-20 degrees C, and of ice VI at about 0.8 GPa/13 degrees C. Both boundaries have a positive sloped course separating three areas of different PVT properties of water. However, this P-T topology is obscured by an unresolved complication in the temperature range of 40-60 degrees C, which allows different topological interpretations of the data. As a cross-check for the compression experiment the dehydration boundary of sodium chloride-dihydrate (NaCl.2H2O) has been determined up to 1.5 GPa. The dehydration curve of NaCl.2H2O which traverses the two anomaly boundaries shows two inflections at the intersection, at 0.27 GPa/12 degrees C and at 0.77 GPa/22 degrees C, respectively. While the isothermal compressibility curves as well as the dP/dT course of the two anomaly boundaries give evidence of two densifications of water, the slope analysis of the inflections of the NaCl-2H2O dehydration curve suggests that the entropy change plays an important role. A recent model of water at high pressure conditions proposes a gradual structural transition from a low density water (LDW) at low pressures to a high density water (HDW) at high pressures. The compression data as well as the inflections of the dehydration boundary indicate, however, two discrete structural changes of water. Data comparison with that model suggests that the anomaly boundary at lower pressure corresponds to a volume fraction [V(HDW)/(V(LDW)+V(HDW))] of 0.8, while the upper one approaches a volume fraction of 1.     

The peculiar kinetics of the reaction between acetylene and the cyclopentadienyl radical

The cyclopentadienyl radical (cC(5)H(5)) is a fascinating molecule characterized by several peculiar properties, such as its high internal symmetry and resonance enhanced stability. This makes cC(5)H(5) one of the most abundant radicals present in high temperature gaseous environments, such as flames. Therefore it is generally considered an interesting candidate as the starting point of reaction pathways leading to the formation of polycyclic aromatic hydrocarbons (PAH) and soot in combustion processes. However, known reaction pathways are not able to explain some recent experimental findings concerning the rapid conversion of cC(5)H(5) into C(7)H(7) and C(9)H(8) in the presence of acetylene. In this work, we used ab initio calculations and quantum Rice-Ramsperger-Kassel (QRRK) theory to investigate the cC(5)H(5) + C(2)H(2) reaction kinetics. We found that cC(5)H(5) can add acetylene to form, through a fast and not previously known reaction, the heptatrienyl radical (cC(7)H(7)), which, in many ways, can be considered the superior homologue of cC(5)H(5). The calculated reaction kinetic constant is (2.2 x 10(11))exp(-6440/T(K)) cm(3) mol(-1) s(-1) and is in good agreement with experimental data, while that of the inverse process is (4.2 x 10(16))T(-1) exp(-30 850/T(K)) s(-1). In a successive reaction, cC(7)H(7) can add a second acetylene molecule to form indene, cC(9)H(8), and H. The forward and backward kinetic constants are (6.6 x 10(11))exp(-10 080/T(K)) and (4.2 x 10(14))exp(-27 300/T(K)) cm(3) mol(-1) s(-1), respectively. These two successive reactions, leading from a single C5 cycle to a bicyclic C5-C6 species, represent a new PAH growth mechanism, characterized by a C5-C7 ring enlargement reaction.     

High-pressure x-ray diffraction and Raman spectroscopy of ice VIII

In situ high-pressure/low-temperature synchrotron x-ray diffraction and optical Raman spectroscopy were used to examine the structural properties, equation of state, and vibrational dynamics of ice VIII. The x-ray measurements show that the pressure-volume relations remain smooth up to 23 GPa at 80 K. Although there is no evidence for structural changes to at least 14 GPa, the unit-cell axial ratio ca undergoes changes at 10-14 GPa. Raman measurements carried out at 80 K show that the nu(Tz)A(1g)+nuT(x,y)E(g) lattice modes for the Raman spectra of ice VIII in the lower-frequency regions (50-800 cm(-1)) disappear at around 10 GPa, and then a new peak of approximately 150 cm(-1) appears at 14 GPa. The combined data provide evidence for a transition beginning near 10 GPa. The results are consistent with recent synchrotron far-IR measurements and theoretical calculations. The decompressed phase recovered at ambient pressure transforms to low-density amorphous ice when heated to approximately 125 K.     

Perovskite, LiNbO3, corundum, and hexagonal polymorphs of (In(1-x)M(x))MO3

LiNbO(3) (LN), corundum (cor), and hexagonal (hex) phases of (In(1-x)M(x))MO(3) (x = 0.143; M = Fe(0.5)Mn(0.5)) were prepared. Their crystal structures were investigated with synchrotron X-ray powder diffraction, and their properties were studied by differential thermal analysis, magnetic measurements, and M?ssbauer spectroscopy. The LN-phase was prepared at high pressure of 6 GPa and 1770 K; it crystallizes in space group R3c with a = 5.25054(7) ?, c = 13.96084(17) ?, and has a long-range antiferromagnetic ordering near T(N) = 270 K. The cor- and hex-phases were obtained at ambient pressure by heating the LN-phase in air up to 870 and 1220 K, respectively. The cor-phase crystallizes in space group R-3c with a = 5.25047(10) ?, c = 14.0750(2) ?, and the hex-phase in space group P6(3)/mmc with a = 3.34340(18) ?, c = 11.8734(5) ?. T(N) of the cor-phase is about 200 K, and T(N) of the hex-phase is about 140 K. During irreversible transformations of LN-(In(1-x)M(x))MO(3) with the (partial) cation ordering, the In(3+), Mn(3+), and Fe(3+) cations become completely disordered in one crystallographic site of the corundum structure, and then they are (partially) ordered again in the hex-phase. LN-(In(1-x)M(x))MO(3) exhibits a reversible transformation to a perovskite GdFeO(3)-type structure (space group Pnma; a = 5.2946(3) ?, b = 7.5339(4) ?, c = 5.0739(2) ? at 10.3 GPa) at room temperature and pressure of about 5 GPa.     

Isentropic partial molal compressibilities of alcohols in propylene carbonate at 25°C

The isentropic coefficients of compressibility of the homologous series of alcohols and diols R _n CH₂OH (n=2–6), CH₃CHOHR _n (n=1–5), 1,2-propanediol, 1,3- 1,4- and 2,3-butanediol, 1,5-pentanediol, and 1,7-heptanediol dissolved in propylene carbonate have been measured at 25°C. Isentropic partial molal compressibilities and group partial molal compressibilities at infinite dilution have been evaluated. The isentropic partial molal compressibilities of these alcohols and diols have been compared with the corresponding values in water. This comparison shows that the values in propylene carbonate are higher than in water by a factor of 10 due to an increased compressibility of the solvation sheath around nonpolar groups in PC.     

Temperature-dependent kinetics study of the gas-phase reactions of OH with n- and i-propyl bromide

An experimental, temperature-dependent kinetics study of the gas-phase reactions of hydroxyl radical with n-propyl bromide, OH+n-C3H7Br-->products (reaction 1), and i-propyl bromide, OH+i-C3H7Br-->products (reaction 2), has been performed over wide ranges of temperatures 297-725 and 297-715 K, respectively, and at pressures between 6.67 and 26.76 kPa by a pulsed laser photolysis/pulsed laser-induced fluorescence technique. Data sets of absolute bimolecular rate coefficients obtained in this study for reactions 1 and 2 demonstrate no correlation with pressure and exhibit positive temperature dependencies that can be represented with modified three-parameter Arrhenius expressions within their corresponding experimental temperature ranges: k1(T)=(1.32x10(-17))T1.95 exp(+25/T) cm3 molecule(-1) s(-1) for reaction 1 and k2(T)=(1.56x10(-24))T4.18exp(+922/T) cm3 molecule(-1) s(-1) for reaction 2. The present results, which extend the current kinetics data base of reactions 1 and 2 to high temperatures, are compared with those from previous works. On the basis of the present data and available data from previous studies, the following bimolecular rate coefficient temperature dependencies can be recommended for the purpose of kinetic modeling: k1(T)=(1.89x10(-19))T2.54exp(+301/T) cm3 molecule-1 s-1 for reaction 1 in a temperature range 210-725 K, and k2(T)=(2.83x10(-21))T3.1exp(+521/T) cm3 molecule(-1) s(-1) and k2(T)=(4.54x10(-24))T4.03exp(+860/T) cm3 molecule(-1) s(-1) for reaction 2 in temperature ranges 210-480 and 297-715 K, respectively.     

Experimental and Theoretical Studies of ScS under Pressure

The compressibilities of ScS and a series of Sc(1)(-)(x)()S metal defect structures (x > 0) were studied using a diamond anvil cell and synchrotron radiation at pressures up to 73 GPa. The results show that the bulk modulus increases with x, in contrast to the usual view that a less dense material is more easily compressed. The results are in qualitative agreement with existing band structure calculations designed to probe the mechanism of the ready metal atom loss from ScS at high temperatures. They are also in agreement with new calculations, both of the tight-binding and the first-principles FLAPW type. Numerically the latter show an increase in the bulk modulus of 30% between ScS and Sc(0.875)S and are in exact numerical agreement with the experimental results.     

Probing the effects of heterogeneity on delocalized pi...pi interaction energies

Dimers composed of benzene (Bz), 1,3,5-triazine (Tz), cyanogen (Cy) and diacetylene (Di) are used to examine the effects of heterogeneity at the molecular level and at the cluster level on pi...pi stacking energies. The MP2 complete basis set (CBS) limits for the interaction energies (E(int)) of these model systems were determined with extrapolation techniques designed for correlation consistent basis sets. CCSD(T) calculations were used to correct for higher-order correlation effects (deltaE(CCSD)(T)(MP2)) which were as large as +2.81 kcal mol(-1). The introduction of nitrogen atoms into the parallel-slipped dimers of the aforementioned molecules causes significant changes to E(int). The CCSD(T)/CBS E(int) for Di-Cy is -2.47 kcal mol(-1) which is substantially larger than either Cy-Cy (-1.69 kcal mol(-1)) or Di-Di (-1.42 kcal mol(-1)). Similarly, the heteroaromatic Bz-Tz dimer has an E(int) of -3.75 kcal mol(-1) which is much larger than either Tz-Tz (-3.03 kcal mol(-1)) or Bz-Bz (-2.78 kcal mol(-1)). Symmetry-adapted perturbation theory calculations reveal a correlation between the electrostatic component of E(int) and the large increase in the interaction energy for the mixed dimers. However, all components (exchange, induction, dispersion) must be considered to rationalize the observed trend. Another significant conclusion of this work is that basis-set superposition error has a negligible impact on the popular deltaE(CCSD)(T)(MP2) correction, which indicates that counterpoise corrections are not necessary when computing higher-order correlation effects on E(int). Spin-component-scaled MP2 (SCS-MP2 and SCSN-MP2) calculations with a correlation-consistent triple-zeta basis set reproduce the trends in the interaction energies despite overestimating the CCSD(T)/CBS E(int) of Bz-Tz by 20-30%.     

Orientation polarization from faster motions in the ultraviscous and glassy diethyl phthalate and its entropy

Dielectric spectra of the beta relaxation in glassy and ultraviscous liquid diethyl phthalate show that its relaxation strength Delta epsilon(beta), the distribution of times, and the relaxation rate are more sensitive to temperature T in the ultraviscous liquid than in the glassy state. The Delta epsilon(beta) against temperature plot has an elbow-shaped break near T(g) of approximately 181 K, which is remarkably similar to that observed in the entropy, enthalpy, and volume against temperature plots, and in the plot of Delta epsilon(beta) against the liquid's entropy minus its 0 K value. The ratio of Delta epsilon(beta) to diethyl phthalate's entropy, after subtracting the 0 K value, is 1.08 x 10(-3) mol K/J in the glassy state at 120.4 K, which decreases slowly to 0.81 x 10(-3) mol K/J at 176 K near T(g) and thereafter rapidly increases to 1.57 x 10(-3) mol K/J at 190 K. Variation in Delta epsilon(beta) parallels the variation of the entropy. A change in the activation energy of the beta process at T>T(g) indicates that its rate is also determined by the structure of the ultraviscous liquid. Features of beta relaxation are consistent with localized motions of molecules and may not involve small-angle motions of all molecules.     

Potentiometric studies of indium(III) azide complexes in aqueous medium

The stability constants of indium-azide complexes were determined by the potentiometric method (glass electrode). The effect monitored was the change in pH of a solution of azide and hydrazoic acid (N(-)(3)/HN(3)) when indium(III) cations were added. The azide concentration was varied from close to zero to 90mM, the ionic strength being kept at 2.000 M with sodium perchlorate and the temperature at 25.0 degrees . Evaluation of experimental data showed only mononuclear species, and the global constants found were beta(1) = (2.0 +/- 0.1) x 10(3), beta(2) = (7 +/- 2) x 10(5), beta(3) = (5 +/- 1) x 10(7) and beta(4) = (7 +/- 3) x 10(8).     

A new approach to suppress nonlinearity-transparency trade-off through coordination chemistry: syntheses and spectroscopic study on second-order nonlinear optical properties of a series of square-pyramidal zinc(II) complexes

Five new square-pyramidal coordination compounds L x Zn(acac)(2) (1-5) (acac = acetylacetonate; L is a variety of thiosemicarbazones: p-dimethylaminobenzaldehyde thiosemicarbazone (1), p-hydroxy-o-methoxybenzaldehyde thiosemicarbazone (2), p-methoxybenzaldehyde thiosemicarbazone (3), p-hydroxybenzaldehyde thiosemicarbazone (4), o-hydroxybenzaldehyde thiosemicarbazone (5)) have been synthesized and characterized by 1H NMR, IR, and elemental analysis. All of these compounds exhibit pretty wide transparent ranges in the visible region. Their electronic absorption spectra have been studied experimentally, and theoretically by ZINDO/S calculation. The latter has also been utilized to estimate the extent of intramolecular charge transfer. The MOPAC software package has been used to evaluate their first-order molecular hyperpolarizabilities (beta). All beta values of the five coordination compounds are larger than those of the corresponding thiosemicarbazones. And complex 1 shows the largest beta(0) (39.1 x 10(-30) esu) in the series.