Experimental Dissociation Research Articles

Thermodynamics of aqueous acetic and propionic acids and their anions over a wide range of temperatures and pressures

The apparent molar volumes of aqueous acetic acid were determined ia density measurements at 298 K<T<573 K and 10 MPa<p<38 MPa. The results were corrected for acid ionization and extrapolated to the standard state of infinite dilution. The new data have been combined with literature values of the standard molar volumes and standard molar heat capacities of acetic and propionic acids, and of acetate and propionate ions. Three correlation models were tested in the description of the standard thermodynamic properties at superambient conditions for the two acids and their anions. The most dependable model, inspired by the fluctuation solution theory, has been selected for generation of the recommended data. Adjustable parameters of the model were obtained by simultaneous correlation of the volumes and heat capacities together with experimental dissociation constants of the acid. It is shown that this model can be used for precise and consistent calculations of standard thermodynamic properties of the two acids and their conjugate ions over a wide range of temperatures and pressures.

Using affinity capillary electrophoresis to evaluate average binding constant of 18-mer diphosphotyrosine peptide to antiphosphotyrosine Fab.

We used affinity electrophoresis in capillaries to investigate the interaction between a monovalent antiphosphotyrosine antibody fragment, antigen-binding fragment (Fab), and a divalent antigen (dAg), an 18-mer diphosphopeptide phosphorylated on two-site tyrosine residues. The migration shift behavior of Fab in electrophoretic solution was observed and the quantitative expression was presented to estimate the arithmetical average value of the intrinsic affinities for two epitopes on the dAg with the Ag binding site on the Fab. In dAg excess, based on measurement of mobility changes of Fab analytes at different dAg concentrations, the experimental average dissociation constant (Kd = 27.7 microM) was calculated. It was also found that the structural variation of the two epitopes for binding specificity to the Ag-binding domain of Fab is not apparent. Moreover, the Kd values of Fab-dAg complexes were measured at higher electric fields and shown to be independent of changes in the electric field. Thus, under conditions where the total dAg concentration is in excess of the total Fab concentration, the method and quantitative expression which we developed is generally useful for the understanding of molecular interaction for an unlabeled monovalent receptor and its divalent ligand in free solution.

Experimental dissociation energies of metal cluster dications and their interpretation in a liquid-drop model with empirical corrections

The dissociation energies of doubly charged silver cluster ions in the size range $9&lt;~n&lt;~25$ are measured by multiple collision induced dissociation. They are compared to the dissociation energies of singly charged clusters. To this end, the latter are used to calculate shell corrections in a macroscopic-microscopic model. Good agreement between the resulting predictions of the dissociation energies of the doubly charged systems and the experimental values is found, which indicates the strong influence of electronic effects on the stability of small silver clusters.

Orbital relaxation and molecular properties of silicon compounds

A model that includes orbital relaxation in ab initio quantum chemical calculations of molecular systems is proposed. The role of orbital relaxation in determination of molecular properties is studied in the following series of silicon compounds: SiHnF{4−n} (n = 0−4), H3SiX, and SiX4 (X = H, Cl, CH3, OH, F). It is shown that orbital relaxation always decreases the total energy of a molecule and leads to better agreement between the calculated and experimental equilibrium distances and dissociation energies. The orbital relaxation effect decreases in the following series of chemical bonds: Si-F > Si-C > Si-O > Si-Cl > SiH. Calculation of the ionization energies of molecules in terms of Koopmans’ theorem including orbital relaxation gives better or worse agreement with experiment. Inclusion of orbital relaxation does not improve the description of the dipole moments of polar molecules. Studying the contribution of orbital relaxation allows one to clarify the role of silicon d-orbitals in the electronic structure of silicon compounds. The silicon d-orbitals are shown to be of independent significance in the formation of chemical Si-O and Si-F bonds.

Theoretical Study of Cation/Ether Complexes: Alkali Metal Cations with 1,2-Dimethoxyethane and 12-Crown-4

Hartree−Fock and second-order perturbation theory methods were used to determine structures and binding enthalpies of complexes formed from a single alkali metal cation (Li+ through Cs+) and one or two 1,2-dimethoxyethane ligands or 12-crown-4. These calculations employed multiple basis sets in order to determine the sensitivity of the results to the completeness in the one-particle basis. The results are compared with recently reported collision-induced dissociation experimental findings. In general, good agreement was found between the experimental and theoretical bond dissociation enthalpies, although for the heavier cations discrepancies of as much as 14 kcal/mol or more were uncovered. Possible reasons for these anomalies are discussed.

A theoretical study on the modes of homolytic bond fragmentation in H nXYH m, HSXY and HS(O)XY systems

Recent studies in the authors' laboratories have involved studies on the formation and reactions of substituted alkoxy radicals derived by the photo-induced homolytic cleavage of the SO bond of substituted alkyl 4-nitrobenzenesulfenates ( 1), and the alkyl radicals formed by the β-scission of the alkoxy radicals. An interesting extension of these studies would be consideration of the homolytic cleavage of the SX and XY bonds in ArSXY and ArS(O)XY systems where X and Y are various combinations of nitrogen, oxygen and sulfur. Ab initio theoretical calculations have been carried out on various parent H-S-X-Y-H and HS(O)XYH systems and on the radical species formed by the homolytic dissociation of the SX and XY bonds using the G2MP2 method in order to determine the relative magnitudes of the homolytic bond dissociation energies (taken as the difference in the sum of the total energies of the product radicals minus the total energy of the parent system, E rexs). For calibration purposes, similar calculations have been carried out on hydrogen peroxide and hydrazine for which experimental homolytic bond dissociation energies have been measured. It is found that, in the latter calculations, the results obtained at the HF/UHF level give very poor correspondence with the experimental values, but the results obtained at the UMP2 and QCISD(T) levels nicely bracket the experimental values. The results of the calculations have given an indication of whether the SX or XY bond prefers to undergo homolytic cleavage. The results of these studies could very well be of significant importance in the areas of both physical and synthetic organic chemistry. In these homolytic cleavage reactions some very interesting radical species are formed, only a few of which have been studied previously experimentally or theoretically. The results of these studies indicate that the preferred mode of homolytic cleavage of the SX and XY bonds is essentially dependent only on the relative stability of the radicals formed in the two modes of homolytic bond cleavage.

β-cyclodextrin bimodal complexes with n-alkylbenzenes and n-alkylcyclohexanes A molecular mechanics study

The bimodal complexation of phenyl- and cyclohexyl-alkanes in β-cyclodextrin has been studied by means of molecular mechanics calculations using Allinger's MM3 force field. The host shows a computed preference for including the phenyl ring when alkyl chains contain less than five carbon atoms; the computed geometry always locates the phenyl ring at the primary hydroxyl group zone (narrower rim). In contrast, the cyclohexyl ring is computed to be either at the narrower or at the wider part of the host cavity. A good qualitative correlation between computed and experimental dissociation constants for related compounds have been obtained.

Gas Phase and Surface Kinetics of Diamond-Like Carbon Films Growth in Pecvd Reactors

AbstractThe surface and gas-phase kinetic of deposition of diamond-like carbon films (DLC) obtained in plasma reactors using methane as precursor was here investigated. Kinetic constants of electronic reactions were evaluated using experimental ionization and neutral dissociation cross sections and the Druyvestein electron distribution function. Kinetic constants for ionic and neutral reactions were found in the literature. Surface reactions were divided into processes involving the impingement of gas-phase radicals or ions from the plasma and desorption or recombination reactions of adsorbed surface species. The kinetic constants of the former processes were evaluated.from the ambipolar theory or from the kinetic theory of gases, while the other kinetic constants were determined from analogy with hydrocarbon chemistry. The exception is the desorption of adsorbed methyl radicals, whose kinetic constant was fitted over experimental data. The predictivity of the model was tested through the simulation of three reactors described in the literature widely differing for operating conditions.

Equilibrium data and thermodynamic modelling of cyclopentane and neopentane hydrates

Cyclopentane and neopentane have only recently been recognised as a potential hydrate former, forming structure-II gas hydrates. However, no information on their hydrate phase boundary or modelling has yet been reported. In this paper, experimental hydrate dissociation data for cyclopentane and neopentane in their binaries and ternaries with methane or/and nitrogen (i.e., methane/cyclopentane, nitrogen/cyclopentane, methane/nitrogen/cyclopentane, methane/neopentane, nitrogen/neopentane, and methane/nitrogen/neopentane) over a wide range of temperature (282–301 K and 276–293 K, respectively) have been reported. The results of comparison with other newly discovered hydrate forming compounds showed that cyclopentane is the strongest hydrate promoter with neopentane in the second place. The predicted hydrate free zone is in good agreement with the experimental data, demonstrating the success of modelling.

Photodissociation studies of C n+ at 193 nm ( n = 5−19) 1

Carbon cluster cations from C n + to C 19 - were generated by laser ablation/ ionization of graphite in the Fourier-transform ICR ion trapping mass spectrometer, and dissociated by excimer laser pulses with photon energy 6.43 eV. Branching ratios and relative apparent cross-sections were determined. Further mechanistic and thermochemical information was sought by several additional approaches, including aging experiments in which dissociation was induced at varying times after ion formation; pump-probe experiments in which an initial pumping laser pulse preceded the photodissociation pulse; and time-resolved photodissociation (TRPD) experiments. The Northwestern strain model for systematizing the energetics of carbon cluster ions was extended and modified to give agreement with experimental and theoretical dissociation energetics of these cluster ions. This was combined with a loose-transition state RRKM-theory picture of dissociation to give a proposed overall interpretation of the dissociation chemistry. The observation of metastable ion dissociation via C 1 loss for C 11 + and C 12 + remains an outstanding puzzle, although a partially satisfactory interpretation is proposed.

Van der Waals Complexes between Boron Trifluoride and Carbon Monoxide: A Theoretical Study

An ab initio study on the 1:1 and 1:2 van der Waals complexes between boron trifluoride and carbon monoxide has been carried out. Full geometry optimizations are performed at the MP2/6-31G* and MP2/D95* levels. The bond energies computed at different levels (MP2, MP4) and with several basis sets (6-31G*, D95*, and aug-cc-pVDZ) range from 3.2 to 3.5 kcal/mol for BF3···CO and from 6.4 to 6.6 kcal/mol for OC···BF3··· CO. The counterpoise-corrected values range from 0.7 to 1.6 kcal/mol for BF3···CO and from 1.3 to 3.1 kcal/mol for OC···BF3···CO. These (gas phase) computed values are consistent with the corresponding experimental dissociation enthalpies as measured in liquefied argon (1.8 and 3.5 kcal/mol). The MP2/6-31G* computed vibrational frequencies agree quite well with the infrared measurements. The analysis of the frequencies together with the energetic data gives theoretical support to some tentative assignments proposed in the infrared studies. The experimental suggestion about the formation of the never observed before BF3··· OC and OC···BF3···CO adducts is theoretically confirmed. A theoretical analysis of the wave functions shows that the weakness of the complexes formed can be ascribed to the small charge transfer detected.

Calculation of the standard partial molal thermodynamic properties of KCl 0 and activity coefficients of aqueous KCl at temperatures and pressures to 1000°C and 5 kbar

Regression of experimental activity coefficient and dissociation constant data reported in the literature with the Hückel (1925) and Setchénow (1892) equations (Helgeson et al., 1981) and the revised HKF equations of state (Tanger and Helgeson, 1988; Shock et al., 1989, 1992) generated parameters and thermodynamic properties of dissociated KCI and KCl 0 at 25°C and 1 bar that can be used to calculate the standard partial molal thermodynamic properties of KCl 0 and the activity coefficients of KCl at temperatures and pressures to 1000°C and 5 kbar.

A Knudsen effusion mass spectrometric study of the molecule Si3N

Condensed phase mixtures (Ge+Si+Si3N4) and (Si+Si3N4) were evaporated from boron nitride Knudsen cells and the partial pressures of Si3N(g),Si2NSi2(g), and Si(g) measured with a mass spectrometer at temperatures between 1770 and 2000 K. The thermal functions for Si3N(g) were calculated from theoretical molecular constants, and the enthalpy change for the dissociation reaction: Si3N(g)=Si2N(g)+Si(g) determined. With the revised atomization enthalpy of Si2N(g), ΔatomHmo=1011±12 kJ mol−1 at T=0 K and 1020±12 kJ mol−1 at T=298.15 K, the atomization enthalpy of Si3N(g) was derived as 1298±19 kJ mol−1 at T=0 and 1312±19 kJ mol−1 at T=298.15 K. These values in combination with the enthalpies of formation of Si(g) and N(g) yielded the enthalpies of formation ΔfHmo at T=298.15 K: 352±15 kJ mol−1 for Si2N(g), and 511±22 kJ mol−1 for Si3N(g). Experimental and theoretical bond dissociation energies have been compared and discussed, indicating a very strong bonding of nitrogen to Si3.

Prediction of the thermodynamic properties of aqueous metal complexes to 1000°C and 5 kb

A large number of aqueous metal complexes contribute significantly to hydrothermal, metamorphic, and magmatic processes in the crust of the Earth. Nevertheless, relatively few thermodynamic data other than dissociation constants ( K) for a few dozen of these complexes have been determined experimentally at elevated temperatures and pressures. The calculations summarized below are intended to supplement these experimental data by providing interim predictions of the thermodynamic properties of supercritical aqueous metal complexes using the revised HKF (Helgeson et al., 1981) equations of state for aqueous species (Tanger and Helgeson, 1988; Shock et al., 1992) and correlations among equations of state parameters and standard partial molal properties at 25°C and 1 bar (Shock and Helgeson, 1988, 1990; Shock et al., 1989). These equations and correlations permit retrieval of the conventional standard partial molal entropies ( S 0 ), volumes ( V 0 ), and heat capacities ( C P 0 ) of aqueous metal complexes at 25°C and 1 bar from published values of log K in the supercritical region and the limited number of experimental dissociation constants available in the literature over relatively short ranges of elevated temperature at P SAT ( P SAT and SAT are used in the present communication to refer to pressures corresponding to liquid-vapor equilibrium for the system H 2O, except at temperatures <100°C, where they refer to the reference pressure of 1 bar). The standard partial molal properties computed in this way can then be used to generate corresponding values of Δ S 0, Δ V 0 , and Δ C P 0 of association, which for similar complexes correlate linearly with S 0, V 0 and C P 0 , respectively, of the constituent cations and ligands at 25°C and 1 bar. Generalizing these correlations and combining them with the equations of state permits prediction of the temperature and pressure dependence of log K and other thermodynamic properties of a large number of aqueous metal complexes. As a consequence, it is possible to retrieve values of log K at 25°C and 1 bar from the results of hydrothermal experiments at higher temperatures and pressures or to predict values of log K at hydrothermal conditions when no experimental data are available at temperatures and pressures above 25°C and l bar. Such predictions can be made for temperatures and pressures from 0°C and 1 bar to 1000°C and 5000 bars.

Spectroscopy of mass-selected rhodium dimers in argon matrices

The absorption (scattering depletion) spectrum and Raman spectra for Rh2 in an argon matrix prepared by the mass selected ion deposition technique have been obtained. The absorption spectrum in the visible region shows a single broad transition centered near 495 nm Resonance Raman spectra obtained by exciting with eight visible lines (457.9–514.5 nm) of an argon ion laser give a single, sharp progression with up to four Stokes transitions. These data give ωe=283.9 (18) cm−1 with ωexe=1.83 (33) cm−1, leading to an experimental dissociation energy of 1.4±0.3 eV. The Raman results are discussed in the context of previous theoretical predictions for the dimer.

Relationships between bond dissociation energies, electron density minima and electrostatic potential minima

The experimental dissociation energies of a group of homonuclear diatomic molecules are found to correlate with computed electron densities ρ(r) and electrostatic potentials V(r) at the bond midpoints, supporting an earlier prediction based on density functional arguments (N. H. March, P. M. Kozlowski and F. Perrot 1990, J. molec. Struct. Theochem, 209, 433). The relationships are generalized to 45 molecules of various types, focusing upon the minima of ρ(r) and V(r) along internuclear axes. Dissociation energies are shown to be related distinctly more closely to the minimum values of V(r) than to those of ρ(r). This complements previous findings for negative monatomic ions as well as the recent observation that the V(r) minima provide the more realistic boundary points between bonded atoms (relative to literature values of covalent radii), and thus further establishes the significance of electrostatic potential axial minima with respect to covalent bonding. In the present work, all calculations were carried out by a density functional procedure (Becke exchange, Lee, Yang and Parr correlation, 6-31G** basis sets).

A 193-nm-laser photofragmentation time-of-flight mass spectrometric study of dimethylsulfoxide

The photodissociation of dimethylsulfoxide [(CH3)2SO] at 193.3 nm has been investigated using the molecular beam time-of-flight (TOF) mass spectrometric technique. In addition to CH3 and SO, CH3SO is also observed as a stable primary product, indicating that CH3SO+CH3 is an important product channel for the 193.3 nm photodissociation of (CH3)2SO. The analysis of the TOF data provides evidence that SO is formed via a stepwise mechanism: (CH3)2SO+hν (193.3 nm)→CH3SO+CH3→2CH3+SO. The analysis also indicates that ≈53% of the primary CH3SO radicals undergo further dissociation to produce CH3+SO, yielding a quantum yield of ≈1.53 for CH3. Within the sensitivity of our experiment, the product channel of CH3SCH3+O is not found. The angular distribution for the formation of CH3SO+CH3 is found to be isotropic, an observation consistent with a predissociation mechanism, in which the dissociation of photoexcited (CH3)2SO is slow compared to its rotational period. The energetics for selected dissociation reactions of (CH3)2SO have also been investigated by ab initio calculations at the G2(MP2) level of theory. The experimental dissociation energy at 0 K (53±2 kcal/mol) for the CH3–SOCH3 bond obtained here is in excellent agreement with the theoretical prediction of 52.6 kcal/mol.

Molecular dynamics simulations of the docking of substituted N5-deazapterins to dihydrofolate reductase.

Orientations of the deazapterin ring and the conformational preferences of groups appended to the deazapterin ring in a set of 8-substituted deazapterin cations docked into the dihydrofolate reductase (DHFR) binding site have been investigated using a methodology based on the simulated annealing technique within molecular dynamics (MD) simulations. Of five possible binding pockets for the 8-substituents, identified from a preliminary manual docking study, one has been definitively eliminated after an analysis of MD trajectories, while another remains uncertain. Using a new method based on standard thermodynamic cycles and a linear approximation of polar and non-polar free energy contributions from MD averages, binding affinities of the different ligands in each binding site have been correlated with experimental dissociation constants. The study has provided insights into structure-activity relationships for use in the design of modified inhibitors of DHFR.

Dissociation of Amides in Strongly Basic Medium of Sodium Methoxide in Dimethyl Sulfoxide-Methanol Mixtures

The dissociation constants of eleven amides have been measured in methanol and its mixtures with dimethyl sulfoxide (10 to 80% v/v) using sodium methoxide as the base. The experimental dissociation constants have been used to construct the H- acidity function as a function of methoxide concentration and composition of the DMSO-MeOH mixture as well as function of methoxide concentration in methanol. Moreover, with the help of construction of acidity function, the functions have been devised for constant sodium methoxide concentrations (0.025, 0.1, and 0.2 mol l-1) and changing composition of the DMSO-MeOH mixture.

Microscopic DNA Flexibility Analysis: PROBING THE BASE COMPOSITION AND ION DEPENDENCE OF MINOR GROOVE COMPRESSION WITH AN ARTIFICIAL DNA BENDING AGENT

We have used an artificial DNA bending agent to monitor the local flexibility of the DNA helix as a function of Mg2+ cation concentration, sequence, and temperature. A DNA bending agent was constructed from a pair of triple helix-forming oligonucleotides connected by a flexible polymeric linker, which, when the linker is short enough, causes a bend in a minor groove region separating the two sites of triple helix formation. The unique aspect of this system is that, since the bent region is not in direct contact with the linker or the triple helix-forming oligonucleotides, the free energy reflecting the bendability of the minor helix groove can be estimated from a comparison of binding affinity between the bent and unbent triple helices. A binding competition experiment and association and dissociation kinetic assays executed at 37 degrees C in the presence of 10 mM Mg2+ have revealed an extremely small difference in binding affinity between bent (50 degrees ) and straight triple helices, suggesting that DNA flexibility with respect to minor groove compression is extremely high and virtually independent of the sequence of the distorted duplex. This unexpectedly small difference in binding affinity was detected over the temperature range from 25 to 65 degrees C, and over a Mg2+ concentration range from 0.3 to 10 mM. Thus, these findings provide evidence that DNA bendability for minor groove compression is inherently high and independent of DNA sequence, temperature, or a 30-fold variation of Mg2+ ion concentration.